Case 2 (A.1.NmC1): MH030053.1


Target: 377 samples Number of changes: 1423
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1336-1337 BC BR coord: 9645 - 9646
Direction L1: >> Initial region span: 1-1336,1337-1423Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.65e-202Rec. model vs L2: 7.12e-11
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1336 188.875633 NaN NaN NaN * * *
A.1.NmC1 0 1422 167.303080 156.656844 2372.686312 1.016323e-14
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1337 10.115561 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_GG|TA, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9778_C|T,
9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G,
9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T,
10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A,
10281_A|G, 10297_A|G, 10303_C|T

Case 2 (A.1.NmC1): MZ604862.1


Target: 377 samples Number of changes: 1429
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1381-1382 BC BR coord: 9963 - 9964
Direction L1: >> Initial region span: 1-1381,1382-1429Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.30e-217Rec. model vs L2: 5.55e-07
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1381 186.252811 NaN NaN NaN * * *
A.1.NmC1 0 1428 169.854422 160.105025 2449.78995 4.397434e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1382 9.629772 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T,
1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T,
1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T,
1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A,
1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C,
2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A,
2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G,
2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T,
2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A,
2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_AT|GC, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G,
3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T,
3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G,
3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T,
4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C,
4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T,
4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A,
4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C,
4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A,
4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T,
4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T,
5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T,
5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C,
5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T,
5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C,
5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A,
5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C,
5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6525, 6527_.|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G,
6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T,
6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C,
7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G,
7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T,
7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT,
7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C,
7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T,
7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A,
7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A,
8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T,
8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T,
8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A,
8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G,
8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT,
8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A,
9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG,
9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9964_9972, 9976_9984, 9987, 9990_9991, 10003_C|A,
10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 2 (A.1.NmC1): OQ714242.1


Target: 377 samples Number of changes: 938
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 279-280, 441-442 BC BR coord: 2172 - 2173, 6705 - 6706
Direction L1: << Initial region span: 1-279,280-288,442-938Gap history (edge excluded): 279-442 -> 288-442
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.75e-24
Rec. model vs L1: 8.09e-37 Rec. model vs L2: 1.78e-77
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 279 27.418853 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 289 10.077917 NaN NaN NaN * * *
A.1.NmC2 0 280 -0.128576 -61.648353 1427.296706 2.018900e-30
A.1.NmC1 0 280 -0.168208 -42.219933 1388.439867 5.539322e-22
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 442 61.036418 NaN NaN NaN * * *
A.1.NmC2 0 476 6.481759 33.397997 1553.204005 1.379943e-24



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2371_C|T, 2380_A|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 6124_T|A, 6127_A|G,
6142_T|A, 6154_A|G, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A,
6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6942_TA|CG, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 2 (A.1.NmC1): ON022368.1


Target: 377 samples Number of changes: 1369
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1268-1269 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1267,1272-1369Gap history (edge excluded): 1267-1272
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.73e-214Rec. model vs L2: 6.84e+01
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1267 156.623302 NaN NaN NaN * * *
A.1.NmC1 0 1369 154.372598 143.595239 2378.809523 0.000003
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1272 11.824012 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6502_A|G,
6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G,
6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T,
6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|C, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T,
6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C,
7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A,
7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C,
7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A,
7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T,
7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G,
7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G,
8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A,
8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T,
8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T,
8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G,
8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T,
9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9952_C|T, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 2 (A.1.NmC1): OP508590.1


Target: 377 samples Number of changes: 850
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 55-56, 96-97 BC BR coord: 648 - 649, 1914 - 1915
Direction L1: << Initial region span: 1-55,56-96,97-850Gap history (edge excluded): 55-97 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.71e-07
Rec. model vs L1: 9.21e-08 Rec. model vs L2: 1.80e-40
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 55 6.27497 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 56 6.531544 NaN NaN NaN * * *
A.1.NmC1 0 97 -0.049142 -8.589761 381.179521 2.713110e-07
A.1.NmC2 0 97 -0.213067 -14.695578 393.391156 6.054797e-10
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 97 48.230111 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 802_A|G, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1915_C|A, 1926_TT|CA,
1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C,
2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T,
2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C,
2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G,
5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5662_A|C, 5668_C|T,
5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T,
6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G,
7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C,
7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A,
7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A,
8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A,
8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A,
8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G,
8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A,
9100_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 2 (A.1.NmC1): OP508602.1


Target: 377 samples Number of changes: 863
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 846-847, 848-849 BC BR coord: 9777 - 9778, 10065 - 10066
Direction L1: >> Initial region span: 1-846,847-848,849-863Gap history (edge excluded): 846-849 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.61e-03
Rec. model vs L1: 4.11e-03 Rec. model vs L2: 3.41e-61
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 846 64.41573 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 847 1.945442 NaN NaN NaN * * *
A.1.NmC1 0 849 -0.138315 -3.435066 84.870132 0.004608 *
A.1.NmC2 0 849 -0.152168 -4.992148 87.984296 0.000973 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 849 0.394383 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 356_G|A, 358_T|C, 361_A|G,
367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G,
511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G,
1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1591_C|T, 1593_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C,
2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G,
2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A,
2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C,
2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T,
2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A,
2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A,
3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 5182_G|A, 5194_C|T,
5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A,
5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G,
5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T,
5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT,
6532_C|G, 6547_C|T, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6764_C|T, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7642_C|A,
7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 8023_A|G, 8030_A|G,
8035_C|T, 8037_G|A, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T,
8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T,
8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G,
8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A,
9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9624_CG|TA, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9946_T|C, 9955_A|G, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10117_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G

Case 2 (A.1.NmC1): OP508604.1


Target: 377 samples Number of changes: 620
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 123-124, 248-249 BC BR coord: 1260 - 1261, 6022 - 6023
Direction L1: << Initial region span: 1-123,124-248,249-620Gap history (edge excluded): 123-249 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.42e-24
Rec. model vs L1: 1.26e-40 Rec. model vs L2: 2.58e-40
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 123 13.567488 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 249 12.922443 NaN NaN NaN * * *
A.1.NmC1 0 124 -0.104767 -45.459141 1482.918281 4.424744e-26
A.1.NmC2 0 124 -0.132300 -102.654967 1597.309935 6.403468e-51
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 249 38.333056 None None None * * *



Target sequence

, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T,
376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T,
517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A,
691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T,
2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C,
3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|C, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 6023_A|G, 6025_T|C,
6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A,
6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC,
8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G,
8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T,
8941_G|A, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 2 (A.1.NmC1): OP508608.1


Target: 377 samples Number of changes: 694
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 272-273, 302-303 BC BR coord: 3141 - 3142, 5181 - 5182
Direction L1: << Initial region span: 1-272,273-302,303-694Gap history (edge excluded): 272-303 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.87e-15
Rec. model vs L1: 2.61e-25 Rec. model vs L2: 2.76e-45
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 272 19.795779 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 273 7.380307 NaN NaN NaN * * *
A.1.NmC1 0 303 -0.079124 -27.807442 677.614884 5.240210e-16
A.1.NmC2 0 303 -0.133633 -53.102423 728.204847 5.418383e-27
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 303 29.974643 None None None * * *



Target sequence

, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 356_G|A, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT,
455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T,
610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C,
766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C,
1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA,
1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G,
1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C,
1444_G|A, 1468_A|G, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C,
2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C,
2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C,
3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C,
3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5182_G|A, 5194_C|T,
5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A,
5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C,
6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C,
6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A,
6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A,
6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6724_C|T, 6745_T|C,
6754_C|T, 6757_TG|CA, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7447_C|T,
7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C,
8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A,
8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T,
8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T,
8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9244_C|A,
9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9624_CG|TA, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|C, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A,
10096_A|G, 10104_C|T, 10111_C|T, 10117_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10210_C|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G

Case 2 (A.1.NmC1): OP508706.1


Target: 377 samples Number of changes: 1455
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1435-1436 BC BR coord: 10360 - 10361
Direction L1: >> Initial region span: 1-1435,1452-1455Gap history (edge excluded): 1435-1452
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.11e-190Rec. model vs L2: 8.76e+04
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1435 169.471333 NaN NaN NaN * * *
A.1.NmC1 0 1428 167.220530 156.140227 2591.719546 0.000002
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1452 3.614437 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA,
1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
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9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10475_A|T, 10521_TG|CA,
10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10614_T|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_AG|CC, 10662_CG|AT,
10669_T|C, 10703_C|T

Case 2 (A.1.NmC1): OP508626.1


Target: 377 samples Number of changes: 756
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 281-282, 314-315 BC BR coord: 3357 - 3358, 5181 - 5182
Direction L1: << Initial region span: 1-281,282-314,315-756Gap history (edge excluded): 281-315 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.24e-13
Rec. model vs L1: 1.57e-22 Rec. model vs L2: 2.80e-50
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 281 19.437666 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 315 5.405617 NaN NaN NaN * * *
A.1.NmC1 0 282 -0.079646 -24.302178 608.604356 1.256847e-13
A.1.NmC2 0 282 -0.163206 -57.928626 675.857251 3.118595e-28
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 315 45.925319 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA,
2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T,
2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A,
2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G,
3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3970_G|C, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G,
5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A,
5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G,
5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5701_T|A, 5713_T|C,
5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 6023_A|G, 6025_T|C,
6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A,
6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG,
8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT,
9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C,
9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 2 (A.1.NmC1): OP508628.1


Target: 377 samples Number of changes: 774
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 712-713, 730-731 BC BR coord: 8953 - 8954, 9572 - 9573
Direction L1: >> Initial region span: 1-712,713-730,731-774Gap history (edge excluded): 712-731 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.43e-04
Rec. model vs L1: 1.93e-04 Rec. model vs L2: 5.64e-31
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 712 44.096877 NaN NaN NaN * * *
A.1.NmC2 0 43 -0.902677 -53.160625 2814.32125 1.815133e-43
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 713 3.366131 NaN NaN NaN * * *
A.1.NmC1 0 731 -0.113550 -5.486271 172.972541 0.000143 *
A.1.NmC2 0 731 -0.128175 -7.902825 177.805650 0.000013 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 731 1.159207 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA,
1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1915_C|A, 1926_TT|CA,
1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C,
2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T,
2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2863_A|G, 2878_A|G, 2881_C|T,
2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|T, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C,
5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T,
7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G,
7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A,
7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T,
8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T,
8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C,
8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G,
8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T,
9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T,
9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G

Case 2 (A.1.NmC1): OP508681.1


Target: 377 samples Number of changes: 1435
BC: A.1.NmC1 + A.1.NmC2 BC BR: 1427-1428 BC BR coord: 10523 - 10524
Direction L1: >> Initial region span: 1-1425,1428-1435Gap history (edge excluded): 1425-1428
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.03e+01 Rec. model vs L2: 1.42e-221
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1425 174.621039 NaN NaN NaN * * *
A.1.NmC2 0 1425 132.103559 72.399198 2799.201604 7.856405e-45 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1428 10.647853 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1375_A|G, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G,
1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G,
2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG,
2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G,
2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A,
2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G,
2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G,
2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A,
2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G,
3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3681_TG|CT, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C,
3901_C|T, 3913_A|G, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3979_T|C, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G,
4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A,
4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T,
4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A,
4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A,
4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C,
4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A,
4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T,
4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A,
5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C,
5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G,
5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C,
5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G,
5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A,
5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G,
5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T,
6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G,
6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T,
6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T,
6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T,
6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A,
6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T,
7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C,
7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T,
7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T,
7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C,
7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7717_T|C, 7721_A|C, 7726_C|A, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G,
7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G,
8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT,
8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G,
8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A,
8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A,
8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C,
8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G,
8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A,
9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G,
9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A,
10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C

Case 2 (A.1.NmC1): OP508646.1


Target: 377 samples Number of changes: 759
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 123-124, 290-291 BC BR coord: 1422 - 1423, 5010 - 5011
Direction L1: << Initial region span: 1-123,124-152,291-759Gap history (edge excluded): 123-291 -> 152-291
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.10e-09
Rec. model vs L1: 6.37e-20 Rec. model vs L2: 3.08e-45
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 123 11.348402 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 153 7.006632 NaN NaN NaN * * *
A.1.NmC1 0 124 -0.102398 -20.187251 1108.374503 3.364454e-09
A.1.NmC2 0 124 -0.126798 -49.480232 1166.960463 6.371737e-22
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 291 46.834624 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 1102_C|A, 1111_G|A, 1117_A|T,
1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A,
1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G,
1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G,
2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G,
3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C,
3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA,
4066_C|T, 4081_T|C, 4087_T|C, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G,
6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6869_G|A, 6874_A|T, 6876_C|T,
6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C,
7141_A|G, 7144_C|T, 7156_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A,
7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G,
8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T,
8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G,
8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T,
8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G,
8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A,
9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A

Case 2 (A.1.NmC1): OP508659.1


Target: 377 samples Number of changes: 874
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 162-163, 314-315 BC BR coord: 1605 - 1606, 5010 - 5011
Direction L1: << Initial region span: 1-162,163-237,315-874Gap history (edge excluded): 162-315 -> 237-315
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.31e-08
Rec. model vs L1: 1.28e-19 Rec. model vs L2: 4.60e-66
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 162 13.004424 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 238 5.637665 NaN NaN NaN * * *
A.1.NmC1 0 191 -0.063914 -19.294106 1054.588211 4.822372e-09
A.1.NmC2 0 163 -0.142154 -51.778874 1119.557748 3.760144e-23
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 315 68.57731 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 799_A|G,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_A|G, 946_G|A, 1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C,
1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T,
1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2833_G|A, 2836_G|A, 2863_A|G,
2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C,
3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G,
3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G,
3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4210_A|T, 4219_A|C, 4228_GC|CT,
4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A,
4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A,
5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T,
5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T,
5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C,
5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5992_C|T, 5995_A|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6439_G|A, 6442_A|G, 6451_AG|GA,
6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G,
6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T,
6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A,
6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT,
7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G,
7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G,
7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G,
7552_C|G, 7571_A|C, 7580_C|T, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC,
8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G,
8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G,
8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_A|C, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG,
8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9232_C|T, 9244_C|A,
9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T,
9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9625_G|A, 9637_C|T, 9646_G|T,
9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T,
9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T,
10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 2 (A.1.NmC1): OP508704.1


Target: 377 samples Number of changes: 1431
BC: A.1.NmC1 + A.1.NmC2 BC BR: 1423-1424 BC BR coord: 10523 - 10524
Direction L1: >> Initial region span: 1-1421,1424-1431Gap history (edge excluded): 1421-1424
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.04e+01 Rec. model vs L2: 5.95e-226
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1421 177.405871 NaN NaN NaN * * *
A.1.NmC2 0 1421 130.072455 70.577648 2798.844703 7.289970e-47 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1424 10.647853 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA,
2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C,
2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A,
2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2770_A|G, 2773_T|A,
2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T,
3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G,
3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G,
3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C,
3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_CTGC|TCAT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_TG|CA, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G,
9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G,
9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G,
10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C

Case 2 (A.1.NmC1): OP508678.1


Target: 377 samples Number of changes: 1440
BC: A.1.NmC1 + A.1.NmC2 BC BR: 1424-1425 BC BR coord: 10523 - 10524
Direction L1: >> Initial region span: 1-1422,1425-1440Gap history (edge excluded): 1422-1425
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.10e-06 Rec. model vs L2: 1.82e-223
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1422 176.000441 NaN NaN NaN * * *
A.1.NmC2 0 1422 130.628159 71.47849 2801.043019 6.745761e-46 *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1425 18.697316 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C,
1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T,
1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
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2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T,
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4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T,
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4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C,
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4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
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4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
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5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
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6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
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7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
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9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G,
9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G,
9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G,
10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10309_C|T, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10614_T|C, 10635_G|A, 10639_C|T,
10647_C|T, 10658_AG|CA, 10662_C|T

Case 2 (A.1.NmC1): OP508698.1


Target: 377 samples Number of changes: 1450
BC: A.1.NmC1 + A.1.NmC2 + A.1.NmC1BC BR: 1433-1434, 1447-1448 BC BR coord: 10523 - 10524, 10657 - 10658
Direction L1: >> Initial region span: 1-1424,1434-1447,1448-1450Gap history (edge excluded): 1424-1448 -> 1424-1434
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.73e-02
Rec. model vs L1: 6.36e-04 Rec. model vs L2: 2.63e-211
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1424 173.595140 NaN NaN NaN * * *
A.1.NmC2 0 1431 151.480149 83.166359 2777.667281 8.376903e-35
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1434 18.107395 NaN NaN NaN * * *
A.1 835 1447 -0.319000 -23.371028 76.742055 5.850527e-18
A.1.NmC1 0 1447 -0.823096 -10.248538 50.497077 2.918358e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1448 -0.374547 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 446_T|C, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C,
649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C,
1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T,
1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G,
1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G,
2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG,
2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G,
2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A,
2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G,
2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G,
2755_T|A, 2761_A|G, 2770_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A,
2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G,
3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C,
3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C,
4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T,
4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A,
4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA,
4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_CTGC|TCAT, 4531_C|T,
4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C,
4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A,
5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T,
5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A,
5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G,
6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G,
7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C,
7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G,
7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T,
7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A,
8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T,
9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T,
9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G,
10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10614_T|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_AG|CC, 10662_C|A, 10703_C|T

Case 2 (A.1.NmC1): OP508680.1


Target: 377 samples Number of changes: 1445
BC: A.1.NmC1 + A.1.NmC2 + A.1.NmC1BC BR: 1428-1429, 1442-1443 BC BR coord: 10523 - 10524, 10657 - 10658
Direction L1: >> Initial region span: 1-1428,1429-1442,1443-1445Gap history (edge excluded): 1428-1443 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.59e-10
Rec. model vs L1: 6.36e-04 Rec. model vs L2: 7.48e-266
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1428 177.863460 NaN NaN NaN * * *
A.1.NmC2 0 1425 98.316722 9.793342 2936.413316 1.482473e-73
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1429 18.107395 NaN NaN NaN * * *
A.1 835 1442 -0.319000 -23.371028 76.742055 5.850527e-18
A.1.NmC1 0 1442 -0.823096 -10.248538 50.497077 2.918358e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1443 -0.374547 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C,
1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A,
1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G,
1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C,
1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T,
2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T,
2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T,
2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A,
2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2626_T|C,
2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A,
2761_A|G, 2770_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A,
2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C,
3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C,
4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C,
4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_CTGC|TCAT,
4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C,
4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A,
4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C,
4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A,
4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5167_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T,
5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T,
5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C,
5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G,
5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A,
5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A,
5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C,
6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C,
6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C,
6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C,
6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_TG|CA, 6622_AC|GT,
6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T,
6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T,
6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C,
7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A,
7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C,
7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A,
7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T,
7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G,
7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T,
8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T,
8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G,
8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10475_A|T, 10477_A|G, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G,
10562_T|C, 10605_A|C, 10607_C|T, 10614_T|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_AG|CC, 10662_C|A, 10703_C|T

Case 2 (A.1.NmC1): OP508695.1


Target: 377 samples Number of changes: 1448
BC: A.1.NmC1 + A.1.NmC2 BC BR: 1432-1433 BC BR coord: 10523 - 10524
Direction L1: >> Initial region span: 1-1423,1433-1448Gap history (edge excluded): 1423-1433
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.10e+10 Rec. model vs L2: 2.71e-213
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1423 176.524080 NaN NaN NaN * * *
A.1.NmC2 0 1430 129.672357 80.732279 2782.535442 2.692980e-37
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1433 8.107395 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
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8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G,
9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G,
9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9938_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T,
10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A,
10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G,
10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10614_T|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_AG|CC, 10662_C|A

Case 2 (A.1.NmC1): OP508686.1


Target: 377 samples Number of changes: 1439
BC: A.1.NmC1 + A.1.NmC2 BC BR: 1428-1429 BC BR coord: 10523 - 10524
Direction L1: >> Initial region span: 1-1419,1429-1439Gap history (edge excluded): 1419-1429
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.59e-01 Rec. model vs L2: 4.95e-207
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1419 176.649871 NaN NaN NaN * * *
A.1.NmC2 0 1426 140.250567 91.310489 2759.379023 9.349362e-33
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1429 13.699858 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|C, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2770_A|G, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A,
2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G,
3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_CTGC|TCAT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A,
6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_TG|CA, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A,
8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A,
8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C,
8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T,
8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A,
9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A,
9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T,
9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A,
9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T,
10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T,
10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T,
10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10475_A|T, 10521_TG|CA, 10528_G|C, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C,
10607_C|T, 10614_T|C

Case 3 (A.1): OQ932914.1


Target: 835 samples Number of changes: 1170
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1151-1152 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1098,1152-1170Gap history (edge excluded): 1098-1152
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.64e-194Rec. model vs L2: 1.48e-36
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1098 13.294905 NaN NaN NaN * * *
A.1 835 3 1.565350 -91.907748 2991.815495 2.772633e-27
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1152 0.968683 None None None * * *



Target sequence

, 71_A|T, 80_A|T, 83_CG|GT, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC,
322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T,
613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G,
904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A,
1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G,
1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG,
1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C,
1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A,
1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A,
1860_C|G, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|A, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C,
2464_C|T, 2467_C|A, 2470_C|A, 2478_G|C, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T,
2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A,
2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T,
2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T,
3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT,
3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4420_A|G,
4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T,
4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5282_.|A, 5287, 5293_C|G, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5321_G|T, 5326_T|C, 5338_C|T, 5344_G|A,
5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G,
5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5649_A|T, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7168_A|G, 7171_G|T, 7174_G|A, 7201_A|G, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C,
7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G,
7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|AC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG,
7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A,
7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A,
7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G,
8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T,
8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T,
8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC,
8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G,
8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T,
8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T,
8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC,
9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9644_G|C, 9646_G|A, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC,
9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG,
9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9985_T|A, 9988_C|A,
9991_A|T, 10003_C|A, 10006_AT|TA, 10018_A|G, 10027_A|C, 10030_A|G, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T

Case 3 (A.1): MH666056.1


Target: 835 samples Number of changes: 1430
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1231-1232 BC BR coord: 8847 - 8848
Direction L1: >> Initial region span: 1-1154,1355-1430Gap history (edge excluded): 1154-1355
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.05e-240Rec. model vs L2: 6.87e-53
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1154 92.967015 NaN NaN NaN * * *
A.1.NmC1 0 560 3.167280 -49.747693 2621.495387 4.246771e-43
A.1 835 4 1.560576 -110.805663 2743.611327 1.294820e-69
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1355 0.551474 None None None * * *



Target sequence

, 166_A|T, 171_G|A, 177_TTCG|CGGA, 186_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_AC|GT, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C,
1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T,
2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T,
2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G,
2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_GG|AA, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A,
2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_A|G, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4154_C|A, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4804_T|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8328_TTAC|GGGT, 8336_AAC|TTT, 8340_A|T, 8342_A|G, 8346_CC|GG, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8484_AG|GA, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G,
8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G,
8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8922_A|T,
8924_CCAAAGT|TTTTCTC, 8934_GGGAAC|TCCCCA, 8941_GG|CA, 8944, 8946_A|T, 8949_A|T, 8951_G|C, 8953_A|C, 8955, 8956_G|C, 8959_.|TT, 8961_T|G, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A,
9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC

Case 3 (A.1): MH666058.1


Target: 835 samples Number of changes: 1430
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1231-1232 BC BR coord: 8847 - 8848
Direction L1: >> Initial region span: 1-1154,1355-1430Gap history (edge excluded): 1154-1355
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.05e-240Rec. model vs L2: 6.87e-53
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1154 92.967015 NaN NaN NaN * * *
A.1.NmC1 0 560 3.167280 -49.747693 2621.495387 4.246771e-43
A.1 835 4 1.560576 -110.805663 2743.611327 1.294820e-69
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1355 0.551474 None None None * * *



Target sequence

, 166_A|T, 171_G|A, 177_TTCG|CGGA, 186_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_AC|GT, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C,
1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T,
2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T,
2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G,
2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_GG|AA, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A,
2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_A|G, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4154_C|A, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4804_T|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8328_TTAC|GGGT, 8336_AAC|TTT, 8340_A|T, 8342_A|G, 8346_CC|GG, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8484_AG|GA, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G,
8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G,
8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8922_A|T,
8924_CCAAAGT|TTTTCTC, 8934_GGGAAC|TCCCCA, 8941_GG|CA, 8944, 8946_A|T, 8949_A|T, 8951_G|C, 8953_A|C, 8955, 8956_G|C, 8959_.|TT, 8961_T|G, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A,
9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC

Case 3 (A.1): ON502428.1


Target: 835 samples Number of changes: 1418
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1172-1173 BC BR coord: 8445 - 8446
Direction L1: >> Initial region span: 1-1172,1181-1418Gap history (edge excluded): 1172-1181
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.91e-184Rec. model vs L2: 1.47e-79
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1172 152.495069 NaN NaN NaN * * *
A.1.NmC1 0 687 30.359312 20.438814 2345.122371 5.612158e-58
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1181 19.417944 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2595_CC|GT, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6010_G|A, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A,
6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG,
6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8447_GG|AT, 8450, 8451_CC|AG, 8457_.|T, 8458_ACAA|TGGC, 8466_CCAT|AGGA, 8472_A|G, 8479_G|A, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A,
8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A,
9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T,
10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): MH018098.1


Target: 835 samples Number of changes: 1024
BC: A.1.NmC2 + A.1.NmC1 BC BR: 880-881 BC BR coord: 9016 - 9017
Direction L1: >> Initial region span: 1-767,881-1024Gap history (edge excluded): 767-881
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.70e-190Rec. model vs L2: 5.90e-62
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 767 49.880450 NaN NaN NaN * * *
A.1.NmC1 0 326 15.321215 -67.148639 2674.297278 1.063068e-43
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 881 8.183121 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|T, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 931_C|T, 934_G|C, 943_A|G,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C,
1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A,
1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G,
1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C,
1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C,
2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C,
2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A,
2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T,
4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C,
4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T,
4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A,
5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T,
5164_T|C, 5182_G|A, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G,
5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6264_A|G, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A,
6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C,
6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T,
6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C,
7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T,
7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T,
7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G,
7942_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A,
8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G,
8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G,
8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C,
8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9010_A|G, 9016_G|A,
9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON502424.1


Target: 835 samples Number of changes: 1134
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 494-495, 505-506 BC BR coord: 4008 - 4009, 5430 - 5431
Direction L1: >> Initial region span: 1-494,495-505,506-1134Gap history (edge excluded): 494-506 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.62e-36
Rec. model vs L1: 5.28e-50 Rec. model vs L2: 8.58e+04
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 494 47.066939 NaN NaN NaN * * *
A.1.NmC1 0 290 12.373643 13.981653 2436.036694 1.082515e-21
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 495 6.893663 NaN NaN NaN * * *
A.1.NmC1 0 506 -0.193512 -60.580501 581.161003 4.965693e-30
A.1.NmC2 0 506 -0.194051 -75.038524 610.077049 2.606643e-36
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 506 15.187522 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1414_C|T, 1423_A|G,
1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A,
1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A,
1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T,
1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A,
1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G,
2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A,
2575_G|A, 2581_A|T, 2595_CC|GT, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C,
3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C,
3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A,
3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G,
3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C,
3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G,
3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T,
3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A,
3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A,
4006_CG|AA, 4009, 4013_T|C, 4018_.|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|T, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT,
7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A,
7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA,
7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A,
8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155,
8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A,
8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A,
8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010,
9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC,
9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9661_T|C, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC,
9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG,
9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON022510.1


Target: 835 samples Number of changes: 1187
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1114-1115 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1104,1121-1187Gap history (edge excluded): 1104-1121
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.82e-190Rec. model vs L2: 9.43e-79
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1104 68.539138 NaN NaN NaN * * *
A.1.NmC1 0 362 17.153198 -62.947686 2859.895372 8.081642e-54
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1121 4.068088 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C,
361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C,
498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C,
670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G,
829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C,
964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1201_C|T, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC,
3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T,
3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A,
3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C,
3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4013_T|C,
4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G,
4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C,
4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T,
4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A,
4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T,
5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G,
5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A,
6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C,
7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G,
8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): MN604280.1


Target: 835 samples Number of changes: 1314
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1115-1116 BC BR coord: 8649 - 8650
Direction L1: >> Initial region span: 1-949,1118-1314Gap history (edge excluded): 949-1118
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.51e-189Rec. model vs L2: 1.82e-85
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 949 80.609698 NaN NaN NaN * * *
A.1.NmC1 0 311 30.060324 -84.561512 2645.123025 1.429780e-59
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1118 14.578369 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_GG|AA, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|T, 4039_G|T, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5329_C|T, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A,
5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A,
6264_A|G, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7299, 7303, 7306, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7393_G|A,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C,
7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7801_C|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010,
9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC,
9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G,
9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MN604284.1


Target: 835 samples Number of changes: 1370
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1296-1297 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1155,1303-1370Gap history (edge excluded): 1155-1303
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.33e-190Rec. model vs L2: 8.35e-84
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1155 171.507458 NaN NaN NaN * * *
A.1.NmC1 0 686 50.368109 17.273679 2699.452643 3.198528e-61
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1303 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_AT|GC, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C,
3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A,
4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T,
6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8341_A|G, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A,
9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022400.1


Target: 835 samples Number of changes: 987
BC: A.1.NmC2 + A.1.NmC1 BC BR: 566-567 BC BR coord: 6186 - 6187
Direction L1: >> Initial region span: 1-404,567-987Gap history (edge excluded): 404-567
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.39e-197Rec. model vs L2: 2.98e-09
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 404 36.528177 NaN NaN NaN * * *
A.1.NmC1 0 272 24.759593 -13.717271 1763.434543 2.365172e-10
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 567 14.246422 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G,
3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G,
3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G,
3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A,
4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C,
4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T,
5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5868_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_AC|GT, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A,
8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010,
9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC,
9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T,
9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G

Case 3 (A.1): ON022381.1


Target: 835 samples Number of changes: 1424
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1393-1394 BC BR coord: 10110 - 10111
Direction L1: >> Initial region span: 1-1392,1394-1424Gap history (edge excluded): 1392-1394
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.41e-193Rec. model vs L2: 4.29e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1392 198.700422 NaN NaN NaN * * *
A.1.NmC1 0 1392 153.258607 142.127739 2515.744522 5.955332e-21 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1394 3.144366 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T,
9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T,
9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_CC|TT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA,
10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022390.1


Target: 835 samples Number of changes: 1422
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1391-1392 BC BR coord: 10110 - 10111
Direction L1: >> Initial region span: 1-1390,1392-1422Gap history (edge excluded): 1390-1392
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.42e-193Rec. model vs L2: 7.36e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1390 197.169730 NaN NaN NaN * * *
A.1.NmC1 0 1390 152.367384 141.236517 2517.526967 1.123784e-20 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1392 3.144366 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C,
4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G,
5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C,
7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G,
7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G,
8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G,
8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G,
10051_G|A, 10066_G|A, 10096_A|G, 10111_CC|TT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10309_C|T

Case 3 (A.1): ON022725.1


Target: 835 samples Number of changes: 1017
BC: A.1.NmC2 + A.1.NmC1 BC BR: 960-961 BC BR coord: 9211 - 9212
Direction L1: >> Initial region span: 1-833,961-1017Gap history (edge excluded): 833-961
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.06e-192Rec. model vs L2: 4.09e-56
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 833 51.448802 NaN NaN NaN * * *
A.1.NmC1 0 421 32.517113 -56.653746 2697.307493 1.832752e-39
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 961 3.722580 NaN NaN NaN * * *
A.1 835 961 1.829215 1.829215 290.341571 2710.802512 * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T,
2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A,
3107_T|C, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C,
3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T,
3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C,
3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC,
3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 5458_A|G,
5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A,
6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9010_A|G, 9016_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): MK882614.1


Target: 835 samples Number of changes: 958
BC: A.1.NmC2 + A.1.NmC1 BC BR: 842-843 BC BR coord: 9465 - 9466
Direction L1: >> Initial region span: 1-493,844-958Gap history (edge excluded): 493-844
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.48e-185Rec. model vs L2: 9.84e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 493 41.242852 NaN NaN NaN * * *
A.1.NmC1 0 363 27.494221 -15.467503 2660.935007 1.198848e-16
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 844 6.45804 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC,
3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C,
3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G,
5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A,
6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_T|C, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C,
9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T,
9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10303_C|T

Case 3 (A.1): MK882616.1


Target: 835 samples Number of changes: 697
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 183-184, 496-497 BC BR coord: 1752 - 1753, 8706 - 8707
Direction L1: << Initial region span: 1-183,184-334,499-697Gap history (edge excluded): 183-499 -> 334-499
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.95e-50
Rec. model vs L1: 1.54e-85 Rec. model vs L2: 2.58e-23
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 183 14.468292 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 335 19.979522 NaN NaN NaN * * *
A.1.NmC1 0 184 -0.008963 -108.665714 2253.331427 2.451842e-51
A.1.NmC2 0 184 -0.130932 -102.753649 2241.507297 9.040094e-49
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 499 15.448538 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1165_TC|CT, 1171_TC|CA, 1174_T|C, 1183_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G,
1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T,
1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A,
1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A,
5530_A|T, 5536_A|C, 5539_G|T, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A,
5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 6211_C|T,
6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6271_T|C, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6407, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7528_T|C,
7531_T|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA,
10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MH030091.1


Target: 835 samples Number of changes: 574
BC: A.1.NmC2 + A.1 BC BR: 400-401 BC BR coord: 3678 - 3679
Direction L1: >> Initial region span: 1-400,464-574Gap history (edge excluded): 400-464
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.60e-157Rec. model vs L2: 1.64e-24
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 400 33.070298 NaN NaN NaN * * *
A.1.NmC1 0 400 32.205520 32.20552 933.58896 0.421052 * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 464 22.618614 NaN NaN NaN * * *
A.1.NmC1 0 514 6.851514 -68.972556 1987.945111 8.549037e-39



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T,
1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A,
1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T,
1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T,
2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G,
2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T,
2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C,
2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G,
5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A,
6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G,
6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T,
6571_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): ON022734.1


Target: 835 samples Number of changes: 1110
BC: A.1.NmC2 + A.1.NmC1 BC BR: 985-986 BC BR coord: 8649 - 8650
Direction L1: >> Initial region span: 1-905,986-1110Gap history (edge excluded): 905-986
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.38e-193Rec. model vs L2: 7.11e-55
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 905 76.262878 NaN NaN NaN * * *
A.1.NmC1 0 363 27.494221 -22.79997 2503.59994 4.553147e-39
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 986 4.25268 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC,
3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC,
3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G,
4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A,
4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A,
4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T,
4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G,
4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT,
7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A,
7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA,
7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T,
9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10036_GA|TG, 10051_G|A, 10096_A|G, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C

Case 3 (A.1): ON022371.1


Target: 835 samples Number of changes: 1368
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1336-1337 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1334,1337-1368Gap history (edge excluded): 1334-1337
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.71e-193Rec. model vs L2: 6.02e-54
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1334 86.284771 NaN NaN NaN * * *
A.1.NmC1 0 596 8.146044 -17.85154 2861.70308 1.204409e-41
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1337 3.264396 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 437_A|G, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 641_C|T, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
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8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A,
8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC,
9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T,
9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A,
10066_G|A, 10090_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G,
10309_C|T

Case 3 (A.1): ON022412.1


Target: 835 samples Number of changes: 1370
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1338-1339 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1336,1339-1370Gap history (edge excluded): 1336-1339
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.71e-193Rec. model vs L2: 3.72e-46
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1336 76.212781 NaN NaN NaN * * *
A.1.NmC1 0 596 8.146044 -18.210475 2864.420951 1.985059e-37
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1339 3.264396 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 437_A|G, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 641_C|T, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_AC|GT, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1446_C|T, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C,
1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T,
2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T,
2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_A|G, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C,
3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T,
4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4804_T|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A,
4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C,
4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A,
5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T,
5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C,
5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A,
5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C,
5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A,
6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T,
6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C,
6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G,
6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G,
6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G,
6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G,
6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7024_T|C, 7027_T|C, 7039_T|C,
7046_T|C, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7606_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A,
7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T,
8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10090_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): OP508715.1


Target: 835 samples Number of changes: 1471
BC: A.1.NmC2 + A.1 BC BR: 1429-1430 BC BR coord: 10354 - 10355
Direction L1: >> Initial region span: 1-1429,1432-1471Gap history (edge excluded): 1429-1432
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.51e-229Rec. model vs L2: 6.37e-107
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1429 151.75488 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1432 8.341603 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 454_TT|CC, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C,
1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T,
1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1352_T|C, 1354_G|A, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A,
1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_AC|GT, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A,
1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T,
2083_T|C, 2086_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G,
2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA,
2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G,
3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3157_A|G, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G,
3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C,
3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A,
3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T,
3727_T|C, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3844_G|A, 3850_C|T, 3860_G|A,
3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_ACC|GTT, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G,
3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G,
4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T,
4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A,
4606_G|A, 4610_A|G, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G,
4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T,
4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T,
5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T,
5197_C|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C,
5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C,
5437_T|C, 5443_C|A, 5449_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C,
5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5620_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G,
5740_G|A, 5760_GA|AG, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G,
5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6541_G|A, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_A|G, 6625_AC|GT, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A,
6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A,
6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6946_T|C, 6957_CTT|TCG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T,
7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A,
7459_T|C, 7463_T|C, 7480_CC|GT, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7612_A|C, 7624_A|G, 7634_C|A,
7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T,
7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7873_C|T, 7879_G|A,
7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G,
8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A,
8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G,
8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T,
8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T,
8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_.|C, 8507, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8874_A|T, 8884_A|G, 8911_G|A,
8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9196_C|T, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C,
9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9832_C|T, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G,
9904_T|A, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A,
10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C,
10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_GC|AT, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T,
10315_T|C, 10330_C|T, 10333_G|C, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10373_T|C, 10382, 10384_.|T, 10386_A|G, 10389_CAC|TTT, 10393_GGTGG|TACAT, 10432_T|A, 10437_C|T, 10442_C|A,
10454_G|A, 10459_G|A, 10463_T|A, 10465_A|C, 10469_TGA|CAC, 10482_GGGA|CACG, 10510_A|C, 10512_T|C, 10515_A|C, 10519_A|G, 10521_T|G, 10523_A|T, 10525_AC|GT, 10531_GA|AG, 10535_T|A, 10549_C|A,
10562_T|C, 10565_C|T, 10605_A|C, 10607_C|T, 10612_G|T, 10635_G|A, 10639_C|T, 10644_A|G, 10647_C|T, 10658_AG|CA, 10662_C|T, 10681_CT|TC, 10783_C|T, 10785_C|G, 10788_C|T, 10794_C|G, 10799_G|A

Case 3 (A.1): ON022406.1


Target: 835 samples Number of changes: 1418
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1406-1407 BC BR coord: 10239 - 10240
Direction L1: >> Initial region span: 1-1405,1407-1418Gap history (edge excluded): 1405-1407
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.90e-194Rec. model vs L2: 6.56e-91
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1405 199.542525 NaN NaN NaN * * *
A.1.NmC1 0 1405 43.609731 33.609731 2798.780539 1.897973e-68 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1407 1.062794 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|C, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1162_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
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8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A,
9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A,
9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T,
9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C,
9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T,
9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_TT|CA, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): MH030079.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1354-1355 BC BR coord: 9761 - 9762
Direction L1: >> Initial region span: 1-1353,1355-1426Gap history (edge excluded): 1353-1355
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.55e-194Rec. model vs L2: 3.79e-26
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1353 183.149928 NaN NaN NaN * * *
A.1.NmC1 0 1282 130.448659 118.340691 2481.318618 1.571518e-24
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1355 5.430981 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 597_A|G, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA,
1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C,
1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C,
1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C,
1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C,
1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T,
2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C,
2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G,
3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT,
3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T,
3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C,
4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG,
4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T,
4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C,
4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A,
4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A,
4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A,
4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T,
4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A,
5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A,
5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G,
5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T,
6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G,
7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C,
7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G,
7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G,
8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G,
8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_AT|GC, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MH030081.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1365-1366 BC BR coord: 9858 - 9859
Direction L1: >> Initial region span: 1-1352,1395-1426Gap history (edge excluded): 1352-1395
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.54e-194Rec. model vs L2: 4.38e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1352 172.021033 NaN NaN NaN * * *
A.1.NmC1 0 1281 130.055802 118.206923 2511.586154 2.152655e-20
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1395 2.652835 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_TC|CT, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7234_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8323_C|T, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_AT|GC, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10010_G|A, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MH030082.1


Target: 835 samples Number of changes: 1427
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1395-1396 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1351,1396-1427Gap history (edge excluded): 1351-1396
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.67e-194Rec. model vs L2: 4.32e-26
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1351 192.281803 NaN NaN NaN * * *
A.1.NmC1 0 1280 140.904756 112.204749 2579.590503 1.789690e-24
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1396 2.652835 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
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9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_AT|GC, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10010_G|A, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10080_A|G, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): ON022378.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1394-1395 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1350,1395-1426Gap history (edge excluded): 1350-1395
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.71e-193Rec. model vs L2: 1.80e-11
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1350 170.168975 NaN NaN NaN * * *
A.1.NmC1 0 1279 139.984958 122.07406 2561.85188 2.634719e-15
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1395 3.264396 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C,
4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G,
5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7231_C|T, 7234_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_AT|GC, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10010_G|A,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022397.1


Target: 835 samples Number of changes: 1362
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1350-1351 BC BR coord: 10239 - 10240
Direction L1: >> Initial region span: 1-1349,1351-1362Gap history (edge excluded): 1349-1351
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.93e-194Rec. model vs L2: 1.06e-86
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1349 191.105532 NaN NaN NaN * * *
A.1.NmC1 0 1349 44.561821 34.561821 2792.876359 2.271513e-64 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1351 1.062794 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|C, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1162_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A,
1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G,
1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C,
1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T,
2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C,
2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G,
3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT,
3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T,
3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C,
4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG,
4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T,
4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C,
4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A,
4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C,
4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C,
4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G,
5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A,
8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T,
8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A,
8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A,
8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A,
9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T,
9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A,
9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T,
10240_TT|CA, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): OQ714299.1


Target: 835 samples Number of changes: 791
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 319-320, 335-336 BC BR coord: 2973 - 2974, 6141 - 6142
Direction L1: >> Initial region span: 1-319,320-335,336-791Gap history (edge excluded): 319-336 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.70e-30
Rec. model vs L1: 6.75e-46 Rec. model vs L2: 1.89e-31
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 319 24.894939 NaN NaN NaN * * *
A.1.NmC2 0 289 24.789598 30.66971 1856.66058 0.001333 *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 320 16.899144 NaN NaN NaN * * *
A.1.NmC1 0 336 -0.078392 -53.630086 1051.260173 2.339969e-31
A.1.NmC2 0 336 -0.133378 -78.391678 1100.783357 4.131225e-42
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 336 12.394609 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A,
2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A,
2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2727_.|C, 2734, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G,
2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 5575_T|G, 5584_A|G, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5716_G|A, 5737_C|G, 5740_G|A, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G,
6634_G|T, 6643_C|T, 6673_T|C, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C,
7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G,
7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G,
8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9010_A|G, 9016_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C,
9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T,
9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G,
10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A,
10222_C|T, 10228_C|A, 10231_C|T

Case 3 (A.1): ON022629.1


Target: 835 samples Number of changes: 1372
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1340-1341 BC BR coord: 10125 - 10126
Direction L1: >> Initial region span: 1-1340,1342-1372Gap history (edge excluded): 1340-1342
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.42e-193Rec. model vs L2: 1.09e-04
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1340 128.739198 NaN NaN NaN * * *
A.1.NmC1 0 1339 110.290312 109.279474 2587.441051 3.536954e-09 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1342 3.144366 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2929_G|A, 2932_G|A,
2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A,
4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A,
4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T,
4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5220_C|T,
5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T,
5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A,
5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T,
5941_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6605_C|T, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G,
6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G,
6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A,
8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022623.1


Target: 835 samples Number of changes: 1371
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1339-1340 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1295,1340-1371Gap history (edge excluded): 1295-1340
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.66e-193Rec. model vs L2: 5.40e-10
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1295 141.006860 NaN NaN NaN * * *
A.1.NmC1 0 1224 118.633365 100.722467 2600.555066 6.494925e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1340 3.264396 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_AT|GC, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10010_G|A,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022280.1


Target: 835 samples Number of changes: 1418
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1344-1345 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1334,1351-1418Gap history (edge excluded): 1334-1351
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.82e-191Rec. model vs L2: 5.94e-99
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1334 188.556288 NaN NaN NaN * * *
A.1.NmC1 0 686 40.491389 15.833993 2706.332015 1.003548e-71
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1351 3.641583 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C,
1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A,
1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A,
1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G,
2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G,
2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A,
2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G,
2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A,
2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C,
2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C,
2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G,
2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T,
3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C,
3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C,
3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A,
4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T,
6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7874_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A,
8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T,
8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A,
8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A,
8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A,
9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T,
9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A,
9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T,
9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C,
9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G,
10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T,
10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MK249066.1


Target: 835 samples Number of changes: 1414
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 616-617, 654-655 BC BR coord: 4530 - 4531, 4734 - 4735
Direction L1: >> Initial region span: 1-615,634-654,655-1414Gap history (edge excluded): 615-655 -> 615-634
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.22e-94
Rec. model vs L1: 1.02e-121 Rec. model vs L2: 6.99e-25
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 615 61.250827 NaN NaN NaN * * *
A.1.NmC1 0 353 22.719302 18.72236 2818.55528 6.893979e-37
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 634 9.476815 NaN NaN NaN * * *
A.1.NmC1 0 655 -0.212890 -209.660278 523.320555 7.733672e-95
A.1.NmC2 0 655 -0.407381 -208.608694 521.217389 2.210014e-94
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 655 50.732782 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2736_ATG|GCA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C,
3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A,
4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A,
4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|A, 4533_T|A, 4540_G|C, 4544_C|T, 4548_T|A, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4632_A|T, 4634_GA|CC, 4637_G|T, 4641_TTTATG|GCGCCA, 4648, 4651_A|T,
4655_CC|TG, 4657_.|C, 4658_G|T, 4662_C|A, 4664_4665, 4667, 4668_TG|GA, 4671_GG|CT, 4711_G|C, 4713_T|C, 4715_C|G, 4717_CA|TC, 4720_A|G, 4722_T|A, 4728_AT|TC, 4735_AA|GC, 4741_A|G, 4744_T|C,
4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T,
4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G,
4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T,
5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C,
5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C,
5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G,
5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A,
5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5926_T|G, 5929_C|T, 5932_C|A,
5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T,
6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G,
6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T,
6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T,
6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G,
6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T,
6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G,
6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C,
7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7504_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A,
7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G,
8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G,
8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A,
8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC,
9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A,
9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|C, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G,
9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G

Case 3 (A.1): OQ714323.1


Target: 835 samples Number of changes: 827
BC: A.1 + A.1.NmC1 BC BR: 277-278 BC BR coord: 5133 - 5134
Direction L1: << Initial region span: 1-119,278-827Gap history (edge excluded): 119-278
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.00e-24 Rec. model vs L2: 1.21e-26
Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 120 9.152208 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 278 30.091746 None None None * * *



Target sequence

, 218_A|G, 225_A|G, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T,
724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C,
856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A,
1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G,
3346_C|T, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A,
3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G,
3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C,
3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3829_A|G, 3832_A|C,
3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A,
3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C,
5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT,
5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A,
5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5584_A|G, 5590_T|C,
5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T,
5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A,
5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6034_C|T, 6037_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6106_C|T, 6115_T|A, 6127_A|G, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C,
6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G,
6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G,
6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T,
6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T,
6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C,
7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A,
7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C,
7463_T|C, 7480_C|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A,
9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C,
9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON022672.1


Target: 835 samples Number of changes: 1214
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1120-1121 BC BR coord: 9211 - 9212
Direction L1: >> Initial region span: 1-987,1121-1214Gap history (edge excluded): 987-1121
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.57e-193Rec. model vs L2: 2.07e-06
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 987 98.470518 NaN NaN NaN * * *
A.1.NmC1 0 1067 81.262823 70.263539 2425.472921 1.078802e-10
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1121 7.941879 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A,
3814_T|C, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T,
3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C,
4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T,
4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G,
4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T,
4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C,
4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A,
5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T,
5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A,
5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G,
5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A,
5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A,
6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C,
6478_T|A, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6605_C|T,
6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T,
6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T,
7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G,
7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A,
8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A,
8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T,
8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C,
8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T,
8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A,
9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9778_C|T,
9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10036_GA|TG, 10051_G|A, 10066_G|A,
10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A,
10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022260.1


Target: 835 samples Number of changes: 1412
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1390-1391 BC BR coord: 10179 - 10180
Direction L1: >> Initial region span: 1-1390,1392-1412Gap history (edge excluded): 1390-1392
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.25e-195Rec. model vs L2: 1.22e-86
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1390 173.622145 NaN NaN NaN * * *
A.1.NmC1 0 686 30.102630 28.514738 2786.970523 9.587364e-64
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1392 1.295326 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2736_ATG|GCA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5522_T|C, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G,
6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C,
6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C,
6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T,
6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T,
6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C,
6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC,
7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7504_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A,
8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A,
9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C,
9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10180_C|T, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G,
10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): ON022586.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1325-1326 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1324,1329-1426Gap history (edge excluded): 1324-1329
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.02e-211Rec. model vs L2: 1.31e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1324 192.328452 NaN NaN NaN * * *
A.1.NmC1 0 1426 151.948546 143.569567 2372.860865 8.346748e-22
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1329 9.425631 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
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9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022657.1


Target: 835 samples Number of changes: 1424
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1392-1393 BC BR coord: 10125 - 10126
Direction L1: >> Initial region span: 1-1392,1394-1424Gap history (edge excluded): 1392-1394
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.42e-193Rec. model vs L2: 3.69e-12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1392 177.585894 NaN NaN NaN * * *
A.1.NmC1 0 1391 142.069340 141.058503 2521.882995 1.372126e-16 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1394 3.144366 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2929_G|A, 2932_G|A,
2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC,
7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A,
8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155,
8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A,
8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A,
8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A,
8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A,
8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T,
8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C,
9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T,
9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G,
9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C,
9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A,
9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G,
9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T,
9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A,
10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G,
10309_C|T

Case 3 (A.1): ON502396.1


Target: 835 samples Number of changes: 1379
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1345-1346 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1345,1347-1379Gap history (edge excluded): 1345-1347
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.47e-192Rec. model vs L2: 2.95e-86
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1345 149.725818 NaN NaN NaN * * *
A.1.NmC1 0 234 22.027855 4.749548 2812.500904 1.091836e-63
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1347 3.144771 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2595_CC|GT, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2736_ATG|GCA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5522_T|C, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T,
6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7504_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A,
8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T,
8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G,
8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A,
9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10105_C|T, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): ON022450.1


Target: 835 samples Number of changes: 1369
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1295-1296 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1285,1302-1369Gap history (edge excluded): 1285-1302
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.31e-190Rec. model vs L2: 2.76e-89
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1285 162.718625 NaN NaN NaN * * *
A.1.NmC1 0 686 40.575595 7.197761 2719.604478 2.960760e-64
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1302 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A,
6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T,
6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022471.1


Target: 835 samples Number of changes: 1314
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1240-1241 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1099,1247-1314Gap history (edge excluded): 1099-1247
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.31e-190Rec. model vs L2: 1.07e-82
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1099 120.618988 NaN NaN NaN * * *
A.1.NmC1 0 403 38.262350 -25.664998 2787.329996 9.069666e-58
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1247 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_AT|GC, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A,
5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5346_G|A, 5359_T|C,
5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A,
5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G,
5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A,
6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG,
6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C,
7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8341_A|G, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G,
9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022479.1


Target: 835 samples Number of changes: 1270
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1199-1200 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1189,1206-1270Gap history (edge excluded): 1189-1206
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.10e-190Rec. model vs L2: 7.22e-82
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1189 108.637334 NaN NaN NaN * * *
A.1.NmC1 0 403 38.580206 -30.043282 2792.086565 6.063883e-57
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1206 3.487295 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C,
5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C,
5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C,
5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G,
5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A,
6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G,
6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C,
6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C,
6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T,
6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T,
6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C,
6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC,
7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527,
7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G,
9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A,
9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10186_G|T,
10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10281_A|G,
10297_A|G, 10309_C|T

Case 3 (A.1): MK882619.1


Target: 835 samples Number of changes: 1314
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1240-1241 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1230,1247-1314Gap history (edge excluded): 1230-1247
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.83e-191Rec. model vs L2: 2.55e-81
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1230 123.257254 NaN NaN NaN * * *
A.1.NmC1 0 403 38.580206 -14.065922 2760.131844 2.362606e-56
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1247 3.641583 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4769_T|C,
4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C,
4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G,
5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT,
7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A,
7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA,
7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A,
8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155,
8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A,
8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G,
9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): ON502401.1


Target: 835 samples Number of changes: 1304
BC: A.1.NmC1 + A.1.NmC2 + A.1.NmC1BC BR: 104-105, 856-857 BC BR coord: 942 - 943, 7026 - 7027
Direction L1: << Initial region span: 1-32,170-856,857-1304Gap history (edge excluded): 32-857 -> 32-170
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.61e-29
Rec. model vs L1: 2.87e-40 Rec. model vs L2: 4.32e-177
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 32 3.70441 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 170 0.984845 NaN NaN NaN * * *
A.1 835 856 0.521783 -53.336107 1886.672215 1.797742e-18
A.1.NmC1 0 801 -4.021368 -81.960052 1943.920103 6.653466e-31
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 857 31.002145 NaN NaN NaN * * *
A.1.NmC2 0 170 8.662182 -11.173684 1202.347368 8.614407e-11



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 437_A|G, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 641_C|T, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_AC|GT, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1239_A|G, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G,
1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1446_C|T, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2593_A|G, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_A|G, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G,
3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT,
3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T,
3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C,
4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG,
4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA,
4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4804_T|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T,
4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T,
5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C,
5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT,
5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A,
5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T,
5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5791_T|C, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A,
5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C,
6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A,
6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G,
6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA,
6454_G|A, 6457_A|G, 6460_T|C, 6466_G|A, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A,
6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C,
6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T,
6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T,
6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7024_T|C, 7027_T|C, 7039_T|C, 7046_T|C, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G,
7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A,
7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T,
7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C,
7579_TC|CT, 7597_A|T, 7600_C|T, 7606_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG,
7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A,
7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A,
7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G,
8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T,
8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T,
8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC,
8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT,
8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON502405.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 104-105, 175-176 BC BR coord: 942 - 943, 1467 - 1468
Direction L1: << Initial region span: 1-32,152-175,176-1426Gap history (edge excluded): 32-176 -> 32-152
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.18e-16
Rec. model vs L1: 3.37e-25 Rec. model vs L2: 5.13e+08
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 32 -1.303814 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 152 1.387974 NaN NaN NaN * * *
A.1.NmC2 0 158 -8.266271 -42.750935 235.501870 3.023852e-18
A.1.NmC1 0 158 -8.295882 -43.705505 237.411009 1.163615e-18
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 176 78.701023 NaN NaN NaN * * *
A.1.NmC1 0 980 30.792154 -11.668504 2845.337009 1.404902e-29



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 437_A|G, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 641_C|T, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_AC|GT, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
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8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA,
10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON022587.1


Target: 835 samples Number of changes: 1427
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1401-1402 BC BR coord: 10140 - 10141
Direction L1: >> Initial region span: 1-1400,1402-1427Gap history (edge excluded): 1400-1402
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.31e-193Rec. model vs L2: 2.60e-39
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1400 153.646748 NaN NaN NaN * * *
A.1.NmC1 0 1227 97.912349 71.432409 2679.135181 4.339343e-32
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1402 2.542314 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 509_T|C, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_T|C, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6379_A|G, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7617_A|G, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AAAA|GGGG, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022503.1


Target: 835 samples Number of changes: 1285
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1211-1212 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1201,1218-1285Gap history (edge excluded): 1201-1218
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.33e-190Rec. model vs L2: 7.90e-82
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1201 112.728508 NaN NaN NaN * * *
A.1.NmC1 0 403 38.580206 -25.862402 2783.724803 6.668202e-57
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1218 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A,
5410_T|G, 5413_T|C, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G,
5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C,
5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A,
6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A,
6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C,
7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T,
7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T,
7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T,
7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C,
7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C,
7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C,
7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C,
7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C,
8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A,
8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C,
8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A,
9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022491.1


Target: 835 samples Number of changes: 1188
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1114-1115 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1104,1121-1188Gap history (edge excluded): 1104-1121
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.33e-190Rec. model vs L2: 2.29e-85
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1104 69.460442 NaN NaN NaN * * *
A.1.NmC1 0 362 17.179250 -73.118778 2882.237555 1.233598e-58
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1121 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1172_C|A, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C,
2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G,
2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A,
2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T,
2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A,
3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T,
3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC,
3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G,
4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A,
4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A,
4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G,
4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T,
4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T,
5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7426_CC|TT, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G,
8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A,
9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022473.1


Target: 835 samples Number of changes: 1322
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1248-1249 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1120,1255-1322Gap history (edge excluded): 1120-1255
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.33e-190Rec. model vs L2: 7.71e-90
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1120 143.329043 NaN NaN NaN * * *
A.1.NmC1 0 682 38.846920 -21.065495 2778.13099 5.490564e-65
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1255 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G,
829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C,
964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
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1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
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2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
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3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
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3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C,
4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A,
4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A,
4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A,
4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA,
4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A,
4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C,
4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A,
4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T,
5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T,
5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G,
5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A,
5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G,
6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A,
6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A,
6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C,
6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T,
6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA,
6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T,
6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T,
7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T,
7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G,
7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G,
8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT,
8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G,
8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G,
8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|T, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A,
9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON502410.1


Target: 835 samples Number of changes: 1109
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1077-1078 BC BR coord: 10128 - 10129
Direction L1: >> Initial region span: 1-1076,1078-1109Gap history (edge excluded): 1076-1078
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.71e-191Rec. model vs L2: 3.88e-68
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1076 55.592362 NaN NaN NaN * * *
A.1.NmC1 0 234 22.027855 -63.464956 2946.929911 4.345255e-48
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1078 2.748883 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2595_CC|GT, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C,
3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G,
3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C,
3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA,
3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C,
4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A,
4375_G|C, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T,
4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC,
4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C,
4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A,
5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6205_C|T, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C,
7498_A|G, 7501_G|A, 7504_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T,
8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G,
8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T,
9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C,
9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G,
9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G,
9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_GA|AG, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA,
10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): ON022502.1


Target: 835 samples Number of changes: 1310
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1236-1237 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1226,1243-1310Gap history (edge excluded): 1226-1243
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.31e-190Rec. model vs L2: 6.97e-84
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1226 112.639209 NaN NaN NaN * * *
A.1.NmC1 0 403 38.580206 -30.683451 2797.366903 5.856315e-59
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1243 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5230_C|G,
5246_T|C, 5257_C|T, 5260_G|A, 5284_G|A, 5287_T|C, 5297_C|T, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A,
5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T,
5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A,
5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T,
6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A,
6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A,
6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A,
6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A,
6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C,
6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T,
6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A,
6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT,
7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G,
7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G,
7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G,
7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7766_T|C, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G,
7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG,
7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C,
8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G,
8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T,
8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T,
8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A,
8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC,
9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T,
9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G,
9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G,
10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G,
10309_C|T

Case 3 (A.1): ON022482.1


Target: 835 samples Number of changes: 1315
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1241-1242 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1231,1248-1315Gap history (edge excluded): 1231-1248
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.31e-190Rec. model vs L2: 8.91e-82
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1231 124.153416 NaN NaN NaN * * *
A.1.NmC1 0 403 38.580206 -14.321906 2760.643811 7.480879e-57
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1248 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T,
4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G,
5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A,
5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5350_A|G, 5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C,
7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G,
7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010,
9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC,
9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC,
9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG,
9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022499.1


Target: 835 samples Number of changes: 1229
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1155-1156 BC BR coord: 9771 - 9772
Direction L1: >> Initial region span: 1-1145,1162-1229Gap history (edge excluded): 1145-1162
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.31e-190Rec. model vs L2: 2.11e-80
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1145 93.288711 NaN NaN NaN * * *
A.1.NmC1 0 362 27.435197 -42.016247 2816.032495 1.781009e-55
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1162 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C,
2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G,
2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A,
2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T,
2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A,
3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T,
3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC,
3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T,
3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3829_A|G, 3832_A|C,
3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G,
3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G,
4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT,
4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C,
4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G,
4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T,
5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA,
5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G,
5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A,
5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T,
5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C,
6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G,
6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T,
6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T,
6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G,
6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G,
6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G,
6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C,
7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C,
7171_GC|TT, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA,
7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A,
7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G,
7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A,
7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A,
7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G,
8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A,
8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G,
8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T,
8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A,
8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG,
8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G,
9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G,
9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G,
9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C,
9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9674_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9811_C|T, 9817_G|A, 9823_G|A,
9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T,
10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022511.1


Target: 835 samples Number of changes: 1137
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1040-1041 BC BR coord: 9211 - 9212
Direction L1: >> Initial region span: 1-909,1041-1137Gap history (edge excluded): 909-1041
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.01e-190Rec. model vs L2: 1.62e-70
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 909 77.287336 NaN NaN NaN * * *
A.1.NmC1 0 427 21.086610 -53.64312 2693.28624 9.063494e-50
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1041 4.877995 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1162_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A,
1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G,
1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C,
1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T,
2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A,
2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C,
2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C,
2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G,
2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T,
3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C,
3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G,
3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A,
3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G,
3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC,
4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A,
4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T,
4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T,
4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A,
4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T,
5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C,
5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C,
5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T,
5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T,
5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C,
6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T,
6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C,
6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G,
6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T,
6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G,
6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G,
6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C,
7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G,
7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T,
7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G,
8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G,
8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9010_A|G, 9016_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G,
9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G,
9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022433.1


Target: 835 samples Number of changes: 1316
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1248-1249 BC BR coord: 9798 - 9799
Direction L1: >> Initial region span: 1-1148,1249-1316Gap history (edge excluded): 1148-1249
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.50e-191Rec. model vs L2: 3.64e-84
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1148 162.587117 NaN NaN NaN * * *
A.1.NmC1 0 685 50.232219 11.514426 2720.971149 6.266862e-62
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1249 4.253144 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C,
4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A,
5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T,
5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A,
5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T,
5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A,
5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5929_C|T, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6160_G|A, 6174_A|G, 6187_A|G,
6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T,
6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T,
6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G,
6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T,
7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G,
7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A,
8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T,
8968_A|G, 8971_A|G, 8980_T|C, 9010_A|G, 9016_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A,
9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9798_AGC|TAT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG,
9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022316.1


Target: 835 samples Number of changes: 1082
BC: A.1.NmC2 + A.1.NmC1 BC BR: 939-940 BC BR coord: 9243 - 9244
Direction L1: >> Initial region span: 1-923,941-1082Gap history (edge excluded): 923-941
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.79e-186Rec. model vs L2: 5.50e-23
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 923 60.925910 NaN NaN NaN * * *
A.1.NmC1 0 388 31.701376 2.394769 2571.210462 1.428367e-18
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 941 14.303485 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C,
361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C,
498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C,
670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G,
829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C,
3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T,
4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T,
4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A,
4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C,
4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A,
4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T,
5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A,
5127_C|G, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T,
5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C,
5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C,
5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C,
6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A,
6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G,
6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA,
6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G,
6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T,
6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T,
6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T,
6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|T, 7114_CC|TT, 7117_T|G,
7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C,
7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C,
7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G,
7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG,
7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A,
7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A,
7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G,
8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T,
8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T,
8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 9142_A|G,
9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G,
9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T,
9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022449.1


Target: 835 samples Number of changes: 1413
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1346-1347 BC BR coord: 9824 - 9825
Direction L1: >> Initial region span: 1-1346,1348-1413Gap history (edge excluded): 1346-1348
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.25e-191Rec. model vs L2: 1.55e-95
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1346 199.437504 NaN NaN NaN * * *
A.1.NmC1 0 1339 41.947622 39.799577 2670.400846 4.669054e-70
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1348 4.118566 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
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8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T,
8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT,
8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A,
9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9825_T|C, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T,
9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022593.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1414-1415 BC BR coord: 10239 - 10240
Direction L1: >> Initial region span: 1-1413,1415-1426Gap history (edge excluded): 1413-1415
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.90e-194Rec. model vs L2: 8.74e-40
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1413 186.975443 NaN NaN NaN * * *
A.1.NmC1 0 1224 127.745185 103.67427 2638.651461 1.466272e-32
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1415 1.062794 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1993_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T,
2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T,
2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG,
3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G,
3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3775_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A,
8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_TT|CC, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022312.1


Target: 835 samples Number of changes: 1427
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1415-1416 BC BR coord: 10239 - 10240
Direction L1: >> Initial region span: 1-1414,1416-1427Gap history (edge excluded): 1414-1416
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.90e-194Rec. model vs L2: 8.07e-40
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1414 187.212365 NaN NaN NaN * * *
A.1.NmC1 0 1225 127.899302 103.828387 2638.343227 1.353539e-32
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1416 1.062794 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3775_C|T, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C,
3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G,
4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T,
4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C,
4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C,
4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C,
4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G,
5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G,
5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A,
9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_TT|CC, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022465.1


Target: 835 samples Number of changes: 1351
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1345-1346 BC BR coord: 10269 - 10270
Direction L1: >> Initial region span: 1-1345,1347-1351Gap history (edge excluded): 1345-1347
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.99e-194Rec. model vs L2: 1.59e-75
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1345 158.001586 NaN NaN NaN * * *
A.1.NmC1 0 404 38.639230 31.456643 2807.086715 1.102059e-55
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1347 0.422097 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
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9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10270_T|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022394.1


Target: 835 samples Number of changes: 1372
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1340-1341 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1338,1341-1372Gap history (edge excluded): 1338-1341
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.71e-193Rec. model vs L2: 1.88e-65
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1338 58.679633 NaN NaN NaN * * *
A.1.NmC1 0 32 3.704410 -68.736985 2975.47397 9.341108e-52
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1341 3.264396 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 437_A|G, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 641_C|T, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_AC|GT, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1446_C|T, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C,
1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T,
2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T,
2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3319_CAA|AGG, 3331_A|G, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_A|G, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054, 4055_T|C, 4059_.|G, 4066_C|T, 4081_T|C, 4087_T|C, 4091_G|A, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T,
4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4804_T|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A,
4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C,
4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A,
5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T,
5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C,
5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A,
5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C,
5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A,
6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T,
6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C,
6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G,
6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G,
6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G,
6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G,
6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7024_T|C, 7027_T|C, 7039_T|C,
7046_T|C, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7606_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A,
7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T,
8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8826_A|G, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10090_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022291.1


Target: 835 samples Number of changes: 1425
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1324-1325 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1323,1328-1425Gap history (edge excluded): 1323-1328
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.02e-211Rec. model vs L2: 2.30e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1323 191.548202 NaN NaN NaN * * *
A.1.NmC1 0 1425 151.838177 143.459199 2373.081603 1.631153e-21
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1328 9.425631 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C,
2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C,
4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A,
4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G,
5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8311_C|T, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022293.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1325-1326 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1324,1329-1426Gap history (edge excluded): 1324-1329
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.02e-211Rec. model vs L2: 6.14e-27
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1324 180.046744 NaN NaN NaN * * *
A.1.NmC1 0 1426 131.477969 123.098991 2417.802019 2.315504e-25
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1329 9.425631 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_T|C, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8311_C|T, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022294.1


Target: 835 samples Number of changes: 1425
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1324-1325 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1323,1328-1425Gap history (edge excluded): 1323-1328
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.02e-211Rec. model vs L2: 1.83e-20
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1323 191.902318 NaN NaN NaN * * *
A.1.NmC1 0 1425 151.850261 143.471283 2373.057435 1.155216e-21
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1328 9.425631 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T,
2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8311_C|T, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G,
9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G,
9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G,
9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A,
10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022733.1


Target: 835 samples Number of changes: 1104
BC: A.1.NmC2 + A.1.NmC1 BC BR: 985-986 BC BR coord: 8649 - 8650
Direction L1: >> Initial region span: 1-905,986-1104Gap history (edge excluded): 905-986
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.61e-193Rec. model vs L2: 7.15e-55
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 905 76.262878 NaN NaN NaN * * *
A.1.NmC1 0 363 27.494221 -22.79997 2503.59994 4.553147e-39
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 986 2.719489 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G,
2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C,
2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3097_CT|TC,
3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|A, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC,
3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G,
4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A,
4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A,
4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T,
4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4948_C|T, 4954_T|G,
4957_C|T, 4960_T|C, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5533_C|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7240_C|A, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT,
7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A,
7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA,
7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G,
9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T,
9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G,
9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G

Case 3 (A.1): ON022286.1


Target: 835 samples Number of changes: 1429
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1405-1406 BC BR coord: 10161 - 10162
Direction L1: >> Initial region span: 1-1405,1406-1429Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.80e-200Rec. model vs L2: 5.86e-46
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1405 185.668543 NaN NaN NaN * * *
A.1.NmC1 0 1227 118.166136 102.980304 2618.039392 1.225150e-36
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1406 2.26753 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G,
946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C,
2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G,
2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2677_C|T,
2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A,
2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G,
3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG,
3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T,
3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T,
3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C, 4669_G|A,
4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C,
6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C,
6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C,
8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9227_T|C, 9232_C|T, 9244_C|G, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A,
9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_TC|CT, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022304.1


Target: 835 samples Number of changes: 1426
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1325-1326 BC BR coord: 9558 - 9559
Direction L1: >> Initial region span: 1-1324,1329-1426Gap history (edge excluded): 1324-1329
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.02e-211Rec. model vs L2: 3.08e-27
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1324 190.145693 NaN NaN NaN * * *
A.1.NmC1 0 1426 141.838177 133.459199 2395.081603 3.003047e-25
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1329 9.425631 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 284_T|C, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA,
1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C,
1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C,
1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C,
1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C,
1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T,
2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C,
2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G,
2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T,
2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G,
3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C,
3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G,
4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A, 4523_C|T, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T,
4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4663_C|A, 4667_T|C,
4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4717_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C,
4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C,
4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G,
5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G,
5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T,
5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T,
6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G,
6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8311_C|T, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG,
9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T,
9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9558_.|C, 9560_TC|CG, 9563_G|C, 9566, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G,
9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): ON022549.1


Target: 835 samples Number of changes: 976
BC: A.1.NmC2 + A.1.NmC1 BC BR: 392-393 BC BR coord: 3273 - 3274
Direction L1: >> Initial region span: 1-392,463-976Gap history (edge excluded): 392-463
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.56e-206Rec. model vs L2: 1.15e-17
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 392 35.361495 NaN NaN NaN * * *
A.1.NmC1 0 866 15.505745 4.134899 867.730202 2.748874e-14
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 463 30.231489 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 297_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C,
1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1141_G|A, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1537_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G,
1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G,
1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G,
2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C,
2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C,
4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G,
4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T,
5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G,
5152_TG|CA, 5155_C|T, 5164_T|C, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G,
5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A,
5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5809_T|A, 5821_A|G, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C,
5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C,
6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T,
6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA,
6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T,
6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T,
7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T,
7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_CA|TC, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G,
7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A,
8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A,
8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T,
8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8743_G|A, 8749_T|C, 8755_G|A,
8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A,
8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9778_C|T, 9787_C|T,
9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A,
9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G

Case 3 (A.1): OP508603.1


Target: 835 samples Number of changes: 640
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 284-285, 451-452 BC BR coord: 3333 - 3334, 8058 - 8059
Direction L1: << Initial region span: 1-283,438-451,452-640Gap history (edge excluded): 283-452 -> 283-438
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.37e-16
Rec. model vs L1: 4.93e-33 Rec. model vs L2: 3.70e-24
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 283 17.900145 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 438 8.346988 NaN NaN NaN * * *
A.1.NmC1 0 452 -0.092719 -35.987005 1419.974009 9.245313e-19
A.1.NmC2 0 452 -0.103621 -71.530620 1491.061239 3.380059e-34
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 452 21.058802 None None None * * *



Target sequence

, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T,
610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C,
766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA,
1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A,
1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G,
1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G,
1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T,
2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G,
2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C,
2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2863_A|G, 2878_A|G,
2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T,
3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T,
3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3333_.|T,
3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C,
4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T,
6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C,
6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG,
6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G,
8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T,
8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G,
8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T,
8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T,
9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A,
10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): JF912179.1


Target: 835 samples Number of changes: 1448
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 18-19, 1434-1435 BC BR coord: 321 - 322, 10532 - 10533
Direction L1: >> Initial region span: 1-18,1425-1434,1435-1448Gap history (edge excluded): 18-1435 -> 18-1425
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.93e-174
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.19e-03
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 18 7.128718 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1425 3.072210 NaN NaN NaN * * *
A.1.NmC1 0 1435 0.000000 -1977.895205 7279.790410 0.000000e+00
A.1.NmC2 0 1434 -0.122999 -463.901573 4251.803146 2.929425e-174
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1435 -3.354312 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|T, 327_A|G,
346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 424_C|T, 427_T|A, 432_T|C, 434_C|T, 448_C|T, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 706_T|C, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 802_A|G, 811_T|C, 826_A|G, 829_G|A, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1094_T|C,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT, 1219_A|G, 1221_CT|AA,
1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G,
1507_T|C, 1516_A|G, 1525_G|T, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1593_G|A, 1606_G|A, 1618_G|A, 1621_A|T, 1642_G|C,
1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1711_C|T, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|C, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1966_G|A, 1969_T|C, 1975_G|A,
1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C,
2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_GA|CT, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|T, 2164_A|G, 2176_T|C, 2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G,
2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2477_G|A, 2488_G|A,
2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2541_A|G, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G,
2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2638_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|T, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2812_G|A, 2821_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G,
2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2920_G|A, 2932_G|A, 2938_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3001_CT|TC, 3013_G|A,
3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3127_G|A, 3133_A|G,
3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3241_G|A, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C,
3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G,
3646_A|G, 3649_TC|CA, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3688_G|A, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C, 3763_G|A,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_GG|CA, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4117_G|A, 4120_CT|AC, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G,
4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4285_A|G, 4289_C|A, 4306_T|C, 4309_C|T, 4333_A|T, 4336_G|A,
4345_G|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4453_A|G, 4480_C|T, 4483_GC|AT,
4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|C, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4547_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T,
4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G,
4711_G|C, 4720_A|G, 4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4798_A|G, 4807_C|T,
4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4891_C|T, 4894_G|A, 4897_C|G, 4900_C|T, 4903_C|T, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4924_C|T, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|C, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A,
5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5053_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5125_G|A, 5134_A|G,
5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|C, 5207_T|C, 5215_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5284_G|A, 5287_T|C,
5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5314_C|T, 5323_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C,
5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A,
5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5639_C|T, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G,
5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5791_T|C, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T,
5872_T|C, 5875_G|A, 5893_A|G, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6023_A|G, 6025_T|C,
6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6113_G|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6253_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6292_T|C, 6310_C|T, 6316_A|G,
6319_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6367_G|A, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6421_G|A, 6430_A|G, 6433_T|C, 6439_G|A,
6451_AG|GA, 6457_A|G, 6460_T|C, 6472_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G, 6544_A|G, 6547_C|T, 6569_C|T,
6597_T|C, 6611_A|G, 6613_A|T, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T,
6745_T|C, 6748_C|T, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T,
6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A,
6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7024_T|C, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7081_G|C, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G,
7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_T|A, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T,
7426_CC|TT, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7456_C|T, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7585_T|C,
7597_A|T, 7612_A|C, 7624_A|T, 7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7690_GT|AC, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A,
7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7837_G|A, 7849_C|T, 7861_T|A,
7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7963_C|T,
7966_T|C, 7969_G|A, 7990_TC|CT, 7996_A|G, 8011_C|T, 8023_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C,
8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|T, 8263_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8362_G|A, 8374_T|C,
8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8494_A|G, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G,
8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8725_A|G,
8743_G|A, 8746_A|G, 8749_T|C, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8821_C|T, 8830_A|G, 8833_A|G, 8836_T|C, 8848_C|T, 8851_A|C, 8860_A|G, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC, 8956_GAA|ACG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8986_T|C, 9009_9010, 9017_.|AA, 9022_G|A, 9031_G|A, 9037_G|A,
9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9112_C|T, 9127_T|C, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9205_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|A, 9295_G|A, 9298_C|T, 9313_C|T, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A,
9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9448_G|A, 9454_A|G, 9460_T|C, 9463_T|C,
9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9499_G|A, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T,
9574_G|A, 9577_G|T, 9590_A|G, 9595_G|A, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9619_G|A, 9625_G|A, 9637_C|T, 9643_T|C, 9646_G|T, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC,
9718_C|T, 9745_G|A, 9749_A|G, 9754_T|C, 9763_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C,
9865_G|A, 9880_C|T, 9898_A|G, 9904_T|A, 9907_C|T, 9910_C|A, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10281_A|G, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10362, 10365_10366,
10368_10372, 10373_T|C, 10376_10379, 10382, 10385, 10391_10397, 10403_C|T, 10408_10416, 10418_C|T, 10421_A|T, 10423_10424, 10426_10430, 10435_10447, 10450_10460, 10465_10476, 10522,
10524_G|A, 10533_A|G, 10535_T|A, 10647_C|T, 10650_G|A, 10658_.|C, 10659_AG|CA, 10662_C|T, 10681_CT|TC, 10738_C|T, 10802_.|T, 10817, 10843_AT|TA, 10847_C|A, 10849_A|G

Case 3 (A.1): JF912181.1


Target: 835 samples Number of changes: 1485
BC: A.1 + A.1.NmC2 + A.1 BC BR: 1440-1441, 1448-1449 BC BR coord: 10314 - 10315, 10360 - 10361
Direction L1: >> Initial region span: 1-1440,1441-1447,1482-1485Gap history (edge excluded): 1440-1482 -> 1447-1482
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.01e-07
Rec. model vs L1: 2.37e+02Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1440 186.31803 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1447 7.581527 NaN NaN NaN * * *
A.1.NmC1 0 1441 -0.119625 -30.914750 79.829500 4.214817e-13
A.1 835 1441 -0.389802 -3.468032 24.936063 3.499377e-01 *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1482 -0.105637 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 178_T|C, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 283_T|C, 294_AA|GG, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 320_T|C, 327_AA|GG, 346_A|G, 349_C|A,
352_G|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 430_T|A, 433_TC|CT, 442_G|T, 445_A|C, 448_C|T, 451_A|G, 454_TT|CC, 457_G|T, 464_C|A, 467_T|C, 475_G|T,
488_T|C, 496_G|C, 499_A|G, 501_AC|GT, 509_T|C, 515_C|T, 517_A|G, 523_G|A, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|T, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C,
628_T|C, 634_T|C, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCTAGAAG, 760_G|A, 763_T|C,
766_G|A, 790_C|T, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 865_C|T, 877_A|G, 883_G|A, 886, 890_G|T, 891_.|G, 892_C|T, 898_C|T,
901_CC|TT, 904_T|A, 910_A|G, 931_C|T, 941_C|T, 943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 997_C|T, 1036_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1066_C|T, 1072_T|G, 1090_T|C, 1102_C|A, 1106_C|T, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_T|C, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1183_T|C, 1204_T|C, 1207_A|C,
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8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CAG, 8510_T|A, 8512_T|C, 8536_C|T, 8551_C|T, 8557_T|C, 8574_A|G, 8578_C|T, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G,
8617_A|G, 8620_TC|CT, 8623_G|A, 8629_T|C, 8632_A|C, 8650_G|A, 8653_C|T, 8656_A|C, 8680_C|T, 8683_T|C, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G,
8773_C|T, 8785_C|T, 8792_C|T, 8797_C|T, 8800_A|G, 8808_A|G, 8815_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|T, 8854_T|C, 8866_T|C, 8874_A|T, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T,
8954_A|C, 8956_GAA|ACG, 8962_G|A, 8971_A|G, 8974_C|T, 9013_A|G, 9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9055_T|A, 9061_A|C, 9067_T|C, 9074_C|T,
9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|G, 9151_A|G, 9154_A|G, 9160_G|T, 9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9184_A|G, 9187_A|C, 9190_T|C, 9196_C|T, 9201_A|G,
9212_A|C, 9214_G|A, 9217_T|A, 9232_C|T, 9235_G|A, 9244_C|A, 9256_C|T, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G, 9331_G|C, 9336_AA|TG,
9358_C|T, 9361_G|A, 9367_A|G, 9379_G|C, 9391_C|T, 9397_A|T, 9406_C|A, 9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G, 9445_C|T, 9467_C|T, 9472_C|T, 9484_CT|TC, 9490_A|G, 9493_C|T, 9497_T|C, 9500_A|G,
9505_A|G, 9511_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9556_T|C, 9559_AT|TG, 9562_A|G, 9566_C|T, 9571_C|A, 9573_GG|AA, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C,
9604_T|C, 9607_C|T, 9610_AC|GT, 9625_G|A, 9637_C|T, 9646_G|C, 9649_C|T, 9652_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9691_C|T, 9709_TA|GC, 9712_A|C, 9745_G|A, 9754_T|C, 9769_C|G,
9775_T|C, 9790_T|C, 9796_A|G, 9817_G|A, 9820_T|C, 9832_C|T, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T, 9898_A|G, 9904_T|G, 9910_C|A, 9913_C|T,
9916_A|G, 9919_C|T, 9938_C|T, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G,
10103_AC|GT, 10129_G|A, 10134_T|C, 10142_A|G, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10174_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10234_C|T, 10240_T|C, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_GC|AT, 10273_AC|GA, 10279_G|A, 10285_C|T, 10291_C|T, 10294_C|T, 10297_A|G, 10312_G|A,
10315_T|C, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10363_C|T, 10365_A|T, 10369_10377, 10381_10382, 10385, 10391_10397, 10403_10406, 10409_10414,
10418_10422, 10425_C|T, 10427_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10466, 10470_10475, 10522, 10524_G|A, 10526_C|T, 10533_A|T, 10535_T|A, 10554_CAC|TGT, 10558_A|G,
10562_T|C, 10605_A|C, 10607_C|T, 10620_A|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10681_C|T, 10738_C|T, 10742_T|C, 10847_C|A

Case 3 (A.1): JF912183.1


Target: 835 samples Number of changes: 1453
BC: A.1.NmC2 + A.1 BC BR: 11-12 BC BR coord: 280 - 281
Direction L1: >> Initial region span: 1-11,1440-1453Gap history (edge excluded): 11-1440
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 4.52e-05
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 11 6.430273 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1440 1.992906 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 286_G|A, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|T,
327_A|G, 346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 424_C|T, 427_T|A, 434_C|T, 448_C|T, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|G, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
625_C|T, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 706_T|C, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCCAGAAG, 763_T|C, 766_G|A,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 811_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G,
904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 950_T|C, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A,
1054_A|G, 1072_T|G, 1084_C|T, 1094_T|C, 1099_C|T, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C,
1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1258_T|C, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T,
1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1525_G|T, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G,
1572_C|A, 1585_A|T, 1593_G|A, 1606_G|A, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T,
1723_G|A, 1729_C|A, 1732_C|T, 1738_A|G, 1741_A|C, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1966_G|A, 1969_T|C, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2014_C|T, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2047_C|T, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2089_A|G, 2095_C|T, 2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_GA|CT, 2116_A|G, 2125_TC|CT, 2128_C|G, 2146_A|G,
2149_G|A, 2152_A|T, 2164_A|G, 2188_A|G, 2193_TG|CA, 2197_A|G, 2201_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C,
2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C,
2410_G|A, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2518_T|C, 2524_C|T, 2527_T|A, 2541_A|G, 2548_C|T,
2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2665_G|A,
2677_C|T, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|T, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2821_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2920_G|A,
2932_G|A, 2938_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3211_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3319_CAAC|AGGT, 3331_A|G,
3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3355_C|T, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A,
3465_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|T, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C,
3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3649_TC|CA, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
3679_T|G, 3682_G|T, 3688_G|A, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C, 3763_G|A, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3826_A|G, 3829_A|G,
3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G,
3985_T|A, 4006_CG|AA, 4013_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_GG|CA, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4099_C|T, 4105_C|G, 4115_C|T, 4117_G|A, 4120_CT|AC,
4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A,
4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4285_A|G, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4345_G|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T,
4387_G|A, 4393_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4450_G|A, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4495_T|C, 4498_G|A, 4504_CC|TA,
4510_T|C, 4519_T|C, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4547_T|C, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A,
4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G,
4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4798_A|G, 4807_C|T, 4810_C|T, 4816_T|C,
4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4891_C|T, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4918_CT|TC, 4921_G|A,
4924_C|T, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5035_T|C,
5038_C|A, 5041_C|T, 5047_C|T, 5053_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5125_G|A, 5134_A|G, 5143_A|G, 5152_TG|CA,
5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|C, 5206_CT|TC, 5212_C|T, 5215_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5284_G|A, 5287_T|C, 5293_C|T,
5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5314_C|T, 5323_T|C, 5326_T|C, 5332_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A,
5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C,
5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5639_C|T, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T,
5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_AT|CC, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T,
5872_T|C, 5875_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C,
6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6067_G|A, 6070_C|T, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6253_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6292_T|C, 6310_C|T,
6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6367_G|A, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6421_G|A, 6430_A|G, 6433_T|C, 6439_G|A,
6451_AG|GA, 6457_A|G, 6460_T|C, 6472_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G, 6544_A|G, 6547_C|T, 6550_T|C,
6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C,
6724_C|T, 6745_T|C, 6748_C|T, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T,
6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A,
6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT,
7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7267_C|T,
7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_T|A, 7405_A|G, 7408_T|C, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T,
7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7456_C|T, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7585_T|C,
7597_A|T, 7612_A|C, 7624_A|T, 7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7690_GT|AC, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A,
7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7837_G|A, 7849_C|T, 7861_T|A,
7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7918_A|G, 7920_AG|GA, 7924_A|G, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7963_C|T,
7966_T|C, 7969_G|A, 7990_T|C, 7996_A|G, 8011_C|T, 8020_C|T, 8023_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G,
8104_A|C, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G,
8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8341_A|G, 8354_C|T, 8356_G|A,
8362_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G,
8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8725_A|G,
8743_G|A, 8746_A|G, 8749_T|C, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8821_C|T, 8826_A|G, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8860_A|G, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC, 8956_GAA|ACG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8986_T|C, 9009_9010, 9017_.|AA, 9022_G|A, 9031_G|A,
9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C,
9190_T|C, 9199_A|G, 9205_G|A, 9208_T|C, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|A, 9295_G|A, 9298_C|T, 9313_C|T, 9319_T|C, 9324_AA|GG,
9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|AC, 9385_A|G, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9448_G|A, 9454_A|G, 9460_T|C,
9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T,
9573_GG|AA, 9577_G|T, 9590_A|G, 9595_G|A, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9625_G|A, 9637_C|T, 9643_T|C, 9646_G|T, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC,
9745_G|A, 9749_A|G, 9754_T|C, 9763_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9865_G|A,
9880_C|T, 9898_A|G, 9904_T|A, 9907_C|T, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10291_C|T, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10362,
10365_10366, 10368_10372, 10373_T|C, 10376_10379, 10382, 10385, 10391_10397, 10403_C|T, 10408_10416, 10418_C|T, 10421_A|T, 10423_10424, 10426_10430, 10435_10447, 10450_10460, 10465_10476,
10488_A|G, 10522, 10524_G|A, 10533_A|G, 10535_T|G, 10738_C|T

Case 3 (A.1): JF912184.1


Target: 835 samples Number of changes: 1441
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 18-19, 1437-1438 BC BR coord: 321 - 322, 10532 - 10533
Direction L1: >> Initial region span: 1-18,1428-1437,1438-1441Gap history (edge excluded): 18-1438 -> 18-1428
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.19e-214
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 3.13e-10
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 18 7.128718 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1428 3.072210 NaN NaN NaN * * *
A.1.NmC1 0 1438 0.000000 -2088.390458 7522.780917 0.000000e+00
A.1.NmC2 0 1437 -0.122999 -549.009661 4444.019322 8.192425e-214
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1438 6.352989 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|T, 327_A|G,
346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 424_C|T, 427_T|A, 432_T|C, 434_C|T, 448_C|T, 451_A|G, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 637_C|T, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 706_T|C, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 811_T|C, 826_A|G, 829_G|A, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1504_A|G, 1507_T|C, 1516_A|G, 1525_G|T, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1561_T|A, 1566_TG|GA, 1570_A|G, 1572_C|A, 1585_A|T, 1593_G|A, 1606_G|A, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1711_C|T, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|C, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C,
1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1966_G|A, 1969_T|A,
1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2063_C|T, 2068_T|C, 2080_A|T,
2083_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_GA|CT, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|T, 2164_A|G, 2176_T|C, 2188_A|G, 2193_TG|CA, 2197_A|G,
2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2290_C|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G,
2314_C|T, 2322_A|G, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A,
2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2541_A|G, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2638_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|T,
2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2759_C|T, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2812_G|A, 2821_G|A, 2827_C|T, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2920_G|A, 2932_G|A, 2938_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C,
3001_CT|TC, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C,
3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3208_C|T, 3211_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A,
3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3355_C|T, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C,
3397_C|A, 3409_G|A, 3412_T|A, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3520_T|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3628_A|C, 3632_C|T,
3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3649_TC|CA, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3688_G|A, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|T, 3739_T|C,
3745_C|T, 3748_T|C, 3763_G|A, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3895_T|A,
3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_GG|CA,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4117_G|A, 4120_CT|AC, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4285_A|G, 4289_C|A, 4306_T|C,
4309_C|T, 4333_A|T, 4336_G|A, 4345_G|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A,
4453_A|G, 4480_C|T, 4483_GC|AT, 4487_G|A, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|C, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4547_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A,
4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4615_G|A, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C,
4798_A|G, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4891_C|T, 4894_G|A, 4897_C|G, 4900_C|T,
4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4924_C|T, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|C, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5024_C|T, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5053_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G,
5119_G|A, 5125_G|A, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|C, 5207_T|C, 5215_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A,
5269_T|C, 5284_G|A, 5287_T|C, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5314_C|T, 5323_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A,
5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5639_C|T, 5641_A|G, 5644_T|G,
5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A,
5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5893_A|G, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C,
6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6113_G|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A,
6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6253_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6292_T|C,
6310_C|T, 6316_A|G, 6319_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6421_G|A, 6430_A|G, 6433_T|C, 6439_G|A,
6451_AG|GA, 6457_A|G, 6460_T|C, 6472_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G, 6544_A|G, 6547_C|T, 6569_C|T,
6597_T|C, 6611_A|G, 6613_A|T, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T,
6745_T|C, 6748_C|T, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T,
6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A,
6979_TC|CT, 6986_C|T, 6991_G|A, 7009_A|T, 7012_G|C, 7015_C|T, 7024_T|C, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT,
7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_GC|TT, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7222_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G,
7267_C|T, 7286_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_T|A, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C,
7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7456_C|T, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT,
7585_T|C, 7597_A|T, 7612_A|C, 7624_A|T, 7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7690_GT|AC, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C,
7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7837_G|A, 7849_C|T,
7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7927_G|A, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG,
7960_C|A, 7963_C|T, 7966_T|C, 7969_G|A, 7990_TC|CT, 7996_A|G, 8011_C|T, 8023_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A,
8101_C|G, 8104_A|C, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|A, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A,
8224_A|G, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8362_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8494_A|G, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8574_A|G,
8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8725_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8821_C|T, 8830_A|G, 8833_A|G, 8836_T|C, 8848_C|T, 8851_A|C, 8860_A|G, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC, 8956_GAA|ACG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8986_T|C, 9009_9010, 9017_.|AA, 9022_G|A,
9031_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9079_A|G, 9082_G|C, 9085_G|C, 9100_G|A, 9112_CC|TT, 9127_T|C, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9205_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|A, 9295_G|A, 9298_C|T, 9313_C|T,
9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9418_C|T, 9424_T|C, 9427_A|G,
9430_A|G, 9448_G|A, 9454_A|G, 9460_T|C, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9499_G|A, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9574_G|A, 9577_G|T, 9590_A|G, 9595_G|A, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9619_G|A, 9625_G|A, 9637_C|T, 9643_T|C, 9646_G|T, 9658_C|T, 9670_C|T,
9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9718_C|T, 9745_G|A, 9749_A|G, 9754_T|C, 9763_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9865_G|A, 9880_C|T, 9898_A|G, 9904_T|A, 9907_C|T, 9910_C|A, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10281_A|G, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G,
10362, 10365_10366, 10368_10372, 10373_T|C, 10376_10379, 10382, 10385, 10391_10397, 10403_C|T, 10408_10416, 10418_C|T, 10421_A|T, 10423_10424, 10426_10430, 10435_10447, 10450_10460,
10465_10476, 10522, 10524_G|A, 10533_A|G, 10535_T|A, 10802_.|T, 10817

Case 3 (A.1): JF912186.1


Target: 835 samples Number of changes: 1445
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 18-19, 1441-1442 BC BR coord: 321 - 322, 10532 - 10533
Direction L1: << Initial region span: 1-3,1432-1441,1442-1445Gap history (edge excluded): 3-1442 -> 3-1432
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.76e-165
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 6.81e-03
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 3 5.083407 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1432 3.072210 NaN NaN NaN * * *
A.1.NmC1 0 1442 0.000000 -2086.668038 7515.336076 0.000000e+00
A.1.NmC2 0 1441 -0.122999 -439.427212 4220.854423 6.797401e-165
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1442 6.352989 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 144_A|G, 166_A|T, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|T, 327_A|G,
346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 424_C|T, 427_T|A, 434_C|T, 439_T|C, 448_C|T, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 501_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 586_G|A, 589_A|G, 595_G|A, 604_C|T,
610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 703_A|T, 706_T|C, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 763_T|C, 766_G|A,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 811_T|C, 826_A|G, 829_G|A, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 922_G|A, 931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A,
1054_A|G, 1072_T|G, 1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT,
1219_A|G, 1221_CT|AG, 1228_G|A, 1231_C|T, 1237_G|A, 1240_C|T, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1339_C|T, 1352_T|C, 1354_G|A, 1363_T|C, 1372_C|T, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1525_G|T, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1593_G|A, 1606_G|A, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A,
1738_A|G, 1741_A|C, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|T, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1951_A|G, 1957_C|A, 1960_C|T, 1966_G|A, 1969_T|C, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2014_C|T, 2017_T|C, 2023_T|C, 2026_A|G, 2029_T|C, 2032_C|T,
2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2089_A|G, 2101_T|C, 2104_C|A, 2110_G|A, 2112_GA|CT, 2116_A|G, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|T,
2164_A|G, 2176_T|C, 2188_A|G, 2193_TG|CA, 2197_A|G, 2201_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T,
2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2518_T|C, 2524_C|T, 2527_T|A, 2541_A|G, 2548_C|T, 2563_A|G,
2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|T, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2758_T|C, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A,
2794_T|C, 2812_G|A, 2821_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2920_G|A, 2932_G|A, 2938_G|A, 2947_A|T, 2950_C|A,
2956_C|T, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3220_T|C, 3226_T|A, 3238_T|C,
3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G,
3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C,
3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3554_G|A, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA,
3613_A|G, 3619_CT|TC, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3649_TC|CA, 3653_C|T, 3655_T|G, 3658_T|C, 3662_C|T, 3667_A|G, 3679_T|G, 3682_G|T, 3691_T|C,
3694_C|T, 3708_A|G, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C, 3763_G|A, 3781_GC|AT, 3784_C|G, 3790_C|G, 3802_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3835_C|T, 3850_C|T, 3860_G|A,
3868_C|A, 3883_T|C, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 3990_C|T, 4006_CG|AA, 4013_T|C,
4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_GG|CA, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4099_C|T, 4105_C|G, 4117_G|A, 4120_CT|AC, 4129_A|G,
4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T,
4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4285_A|G, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4345_G|A, 4351_T|A, 4360_A|T, 4366_A|G, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A,
4393_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|C,
4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4547_T|C, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T,
4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4708_G|A, 4711_G|C, 4720_A|G, 4735_A|G,
4741_A|G, 4744_T|C, 4747_C|T, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4798_A|G, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4891_C|T, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4924_C|T, 4930_G|T, 4939_G|A,
4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|G, 5053_C|T,
5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5125_G|A, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T,
5197_C|T, 5200_A|C, 5207_T|C, 5212_C|T, 5215_G|A, 5230_C|G, 5239_T|A, 5245_G|A, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5284_G|A, 5287_T|C, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5314_C|T,
5323_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T,
5431_T|C, 5437_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A,
5548_T|C, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5639_C|T, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G,
5752_C|T, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5923_T|C, 5926_T|G,
5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C,
6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6113_G|A, 6124_T|A, 6127_A|G, 6135_T|C, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T,
6220_T|C, 6223_G|A, 6229_A|G, 6235_C|T, 6241_T|C, 6244_T|A, 6253_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6292_T|C, 6307_C|T, 6310_C|T, 6316_A|G, 6319_A|G, 6322_G|A,
6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6367_G|A, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6421_G|A, 6430_A|G, 6433_T|C, 6439_G|A, 6451_AG|GA, 6457_A|G,
6460_T|C, 6472_A|G, 6478_T|A, 6481_T|C, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G, 6544_A|G, 6547_C|T, 6550_T|C, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T,
6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6748_C|T, 6757_TG|CA,
6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T,
6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T,
7318_CG|TA, 7324_C|T, 7327_T|G, 7357_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_T|A, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T,
7453_G|A, 7456_C|T, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7585_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7630_A|G,
7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7690_GT|AC, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A,
7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7837_G|A, 7849_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G,
7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7963_C|T, 7966_T|C, 7969_G|A, 7990_TC|CT,
7996_A|G, 8011_C|T, 8020_C|T, 8023_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_AT|GC, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T,
8275_G|A, 8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8299_C|T, 8305_T|A, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8356_G|A, 8362_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T,
8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8503_C|T,
8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C,
8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8725_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8764_A|G, 8773_C|T, 8782_G|A,
8788_C|T, 8792_C|T, 8815_A|G, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8860_A|G, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC,
8956_GAA|ACG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8986_T|C, 9009_9010, 9017_.|AA, 9022_G|A, 9031_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A,
9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9205_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A,
9265_C|A, 9274_A|G, 9277_C|T, 9280_T|A, 9298_C|T, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G, 9331_G|A, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G,
9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9448_G|A, 9454_A|G, 9460_T|C, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9566_C|T, 9573_GG|AA, 9577_G|T, 9590_A|G, 9595_G|A, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9625_G|A, 9637_C|T,
9643_T|C, 9646_G|T, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9763_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A,
9817_G|A, 9823_G|A, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9865_G|A, 9880_C|T, 9898_A|G, 9904_T|A, 9907_C|T, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9952_C|T, 9955_A|G, 9970_A|G,
9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10140_AAA|GGG, 10144_A|G, 10148_A|C, 10153_T|C, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G,
10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10362, 10365_10366, 10368_10372, 10373_T|C, 10376_10379, 10382, 10385, 10391_10397, 10403_C|T, 10408_10416, 10418_C|T, 10421_A|T, 10423_10424,
10426_10430, 10435_10447, 10450_10460, 10465_10476, 10522, 10524_G|A, 10533_A|G, 10535_T|A, 10802_.|T, 10817

Case 3 (A.1): MF004382.1


Target: 835 samples Number of changes: 1483
BC: A.1 + A.1 BC BR: 1465-1466 BC BR coord: 10468 - 10469
Direction L1: >> Initial region span: 1-1460,1481-1483Gap history (edge excluded): 1460-1481
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.71e-10
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1460 200.937916 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1481 1.043567 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 178_T|C, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C, 327_A|G,
346_A|G, 349_C|A, 352_G|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 430_T|A, 433_TC|CT, 442_G|T, 445_A|G, 448_C|T, 451_A|G, 454_T|C, 467_T|C, 475_G|T, 488_T|C,
496_G|T, 499_A|G, 501_A|G, 514_CC|TT, 517_A|G, 523_G|C, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 628_T|C, 634_T|C,
637_C|T, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 757_C|T, 760_G|A, 763_T|C,
766_G|A, 790_C|T, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 871_T|C, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 892_C|T, 898_C|T,
901_CC|TT, 904_T|G, 910_A|G, 931_C|T, 940_CC|TT, 943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 967_C|T, 973_A|G, 985_T|A, 991_T|A, 1036_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|T,
1072_T|G, 1090_T|C, 1102_C|A, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1183_T|C, 1189_C|T, 1204_T|C, 1207_A|T, 1210_G|A,
1216_CC|TT, 1219_A|G, 1222_T|C, 1228_G|A, 1234_A|G, 1237_G|A, 1240_CA|TC, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G, 1282_T|C, 1294_A|G, 1300_G|A,
1306_G|A, 1309_C|T, 1321_C|T, 1333_T|C, 1342_A|G, 1345_C|T, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1433_A|G, 1435_C|T,
1438_C|T, 1453_G|A, 1471_C|T, 1474_C|T, 1480_A|G, 1482_TC|CT, 1491_T|C, 1495_G|A, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1519_C|T, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|A, 1534_G|A, 1544_G|A,
1546_T|C, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T,
1693_C|A, 1701_G|A, 1705_AC|GT, 1723_G|A, 1732_CT|TC, 1738_A|G, 1747_T|C, 1760_A|C, 1765_T|C, 1782_A|G, 1785_A|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C,
1819_T|A, 1822_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1879_C|T, 1887_T|C, 1900_C|T, 1906_T|A, 1915_C|A, 1926_TT|CC, 1946_T|C, 1951_A|G, 1963_C|T, 1969_T|C, 1978_A|G, 1990_T|C,
1993_T|C, 1996_A|G, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2053_T|G, 2059_A|G, 2063_C|T, 2080_A|C, 2083_T|C, 2086_T|C,
2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2112_GA|CG, 2116_A|G, 2119_T|C, 2122_A|T, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G, 2188_A|G, 2193_T|C, 2197_A|G, 2209_C|T, 2215_A|G,
2218_CA|TG, 2221_C|T, 2224_C|A, 2230_T|C, 2239_C|T, 2248_G|A, 2251_C|T, 2257_T|A, 2260_G|A, 2266_G|A, 2275_T|A, 2278_T|C, 2280_C|T, 2290_C|T, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_AC|GT,
2350_G|A, 2353_A|C, 2356_T|C, 2376_CA|TG, 2380_A|G, 2395_C|T, 2401_C|T, 2408_T|C, 2413_A|T, 2419_G|C, 2432_T|C, 2437_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2467_C|A, 2481_A|G, 2488_G|A, 2494_G|A,
2497_C|T, 2500_A|G, 2506_TA|AG, 2515_A|C, 2518_T|C, 2521_A|G, 2524_C|T, 2527_T|G, 2533_C|T, 2537_C|T, 2548_C|T, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|T, 2593_A|G, 2599_T|C, 2602_T|C, 2605_A|G,
2620_CC|TT, 2626_T|C, 2632_T|C, 2635_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C,
2725_G|A, 2728_T|C, 2731_A|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|T, 2767_C|T, 2776_G|T, 2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2809_T|C, 2824_C|T,
2827_C|T, 2833_G|A, 2836_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 3007_T|G, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3169_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G, 3271_A|G, 3289_T|C, 3298_G|A, 3301_T|C,
3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|TGG, 3328_T|C, 3334_G|T, 3337_A|G, 3349_A|G, 3358_G|C, 3361_T|C, 3364_C|T, 3370_AG|GA, 3373_T|C, 3382_A|G, 3394_C|A, 3397_C|A, 3403_A|G,
3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3511_A|G, 3514_AA|GG, 3517_A|C,
3523_T|A, 3535_TT|GC, 3566_G|T, 3569_C|T, 3571_A|G, 3573_G|A, 3576_AA|GG, 3589_A|C, 3598_G|A, 3601_G|A, 3610_AG|CA, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3658_TT|CC, 3667_A|G, 3670_CAC|TGT, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3727_T|C, 3733_G|C, 3739_T|C,
3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3760_A|G, 3763_G|A, 3778_T|C, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3817_G|A, 3820_GA|AG, 3824_C|T, 3826_A|T, 3832_A|T, 3847_T|A, 3851_T|C, 3856_T|C,
3860_G|A, 3868_C|A, 3871_C|G, 3883_TC|CT, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3940_A|G, 3945_ATA|GCG, 3953_T|C, 3959_C|T, 3961_C|G, 3967_TC|GT,
3982_C|G, 3985_T|A, 4006_CG|AA, 4009_A|G, 4013_T|C, 4021_TG|CA, 4030_T|C, 4045_T|C, 4054_T|C, 4056_TC|CA, 4066_C|T, 4075_G|A, 4081_T|C, 4084_A|G, 4087_T|C, 4105_C|G, 4108_A|T, 4120_C|A,
4129_A|G, 4142_C|T, 4150_A|C, 4153_TC|CA, 4159_A|G, 4165_C|A, 4171_T|C, 4174_G|A, 4183_T|C, 4204_C|T, 4210_A|G, 4219_A|C, 4229_C|T, 4234_A|G, 4246_T|C, 4264_C|T, 4267_T|G, 4270_T|C,
4273_GA|AG, 4289_C|A, 4291_C|T, 4304_G|A, 4306_T|C, 4321_G|A, 4324_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4411_A|C, 4423_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_AG|GA, 4456_G|C, 4465_C|T, 4469_G|A, 4474_G|C, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CA,
4528_G|A, 4531_C|T, 4540_G|T, 4544_C|T, 4547_T|C, 4549_T|C, 4557_G|A, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G, 4600_T|A, 4603_T|C, 4605_AG|CA, 4609_CA|TG, 4612_C|T,
4618_A|G, 4627_TC|CT, 4630_G|A, 4651_A|T, 4660_A|G, 4663_C|T, 4666_CT|TC, 4669_G|A, 4678_C|T, 4684_A|G, 4711_G|C, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A,
4769_T|C, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4792_A|C, 4813_T|C, 4819_C|T, 4829_T|C, 4834_A|G, 4840_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4873_G|T, 4876_T|C, 4878_TT|CC, 4882_A|C,
4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|C, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4978_C|T, 4981_T|C, 4984_A|T, 4987_A|C, 4993_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5014_G|A, 5020_T|A, 5024_C|T, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5103_A|G, 5107_G|A, 5113_C|T, 5116_A|G,
5119_G|A, 5140_A|G, 5152_TG|AA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|G, 5176_T|C, 5179_G|A, 5182_G|A, 5185_A|T, 5188_A|G, 5191_T|C, 5193_TC|AT, 5197_C|G, 5200_A|C, 5206_CT|TC, 5212_C|T,
5215_G|A, 5218_C|T, 5230_CT|GC, 5239_T|G, 5245_GT|TC, 5251_C|T, 5257_C|T, 5272_T|C, 5275_A|G, 5287_T|C, 5293_C|T, 5299_G|A, 5302_C|T, 5305_G|A, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G,
5335_C|T, 5344_G|A, 5346_GA|AG, 5368_C|T, 5371_T|C, 5380_A|G, 5383_T|A, 5393_T|C, 5398_A|G, 5407_G|A, 5410_T|G, 5413_T|G, 5416_C|T, 5422_A|G, 5428_C|T, 5431_T|C, 5440_A|G, 5443_C|T, 5452_G|A,
5458_A|G, 5461_T|C, 5464_C|T, 5470_C|A, 5473_T|C, 5479_T|C, 5500_G|A, 5530_A|T, 5539_G|C, 5542_T|A, 5545_G|A, 5549_A|G, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T, 5602_A|T,
5605_C|T, 5623_A|G, 5626_G|T, 5639_C|T, 5641_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5689_A|G, 5701_T|A, 5708_T|C, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_CC|GT, 5740_G|A, 5749_A|G, 5758_G|A,
5760_G|A, 5764_A|G, 5773_G|A, 5776_A|T, 5779_G|A, 5797_T|C, 5800_A|C, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A,
5935_A|T, 5938_C|T, 5941_T|C, 5947_T|C, 5953_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6013_T|A, 6023_A|G, 6025_T|C,
6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6067_G|A, 6100_C|T, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6140_C|A, 6142_T|A, 6145_T|C, 6154_AC|GT, 6157_G|A, 6160_G|A,
6169_G|A, 6172_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6229_A|G, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6280_C|T, 6283_T|A, 6292_T|C, 6310_C|T, 6316_A|G,
6334_T|C, 6346_A|G, 6351_A|G, 6356_C|T, 6361_C|G, 6367_G|A, 6373_T|C, 6379_A|G, 6385_G|T, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G, 6433_T|C,
6439_G|A, 6442_A|G, 6445_T|G, 6448_T|A, 6451_A|G, 6463_G|A, 6472_A|G, 6478_T|A, 6490_T|C, 6493_A|G, 6496_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6529_CC|TT, 6532_CC|GA, 6547_C|T, 6550_T|C,
6569_C|T, 6571_A|G, 6595_A|G, 6611_A|G, 6613_A|T, 6616_G|A, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6649_T|C, 6664_A|G, 6667_C|A, 6673_T|C, 6682_T|C, 6688_G|A, 6703_C|T, 6706_CT|TA,
6709_T|C, 6715_T|C, 6724_C|T, 6730_A|G, 6733_C|T, 6745_T|C, 6757_TG|CA, 6760_C|T, 6766_C|G, 6781_G|A, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6859_CC|TT, 6866_C|T, 6874_A|C, 6876_C|T, 6889_C|T, 6892_G|A, 6895_A|G, 6898_C|T, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G,
6919_G|A, 6925_C|T, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6952_T|C, 6955_TG|CA, 6958_TT|CG, 6969_G|A, 6976_G|A, 6986_C|T, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G,
7030_A|G, 7046_T|C, 7054_C|T, 7063_A|G, 7066_C|T, 7069_A|G, 7079_C|T, 7084_T|C, 7096_A|T, 7105_A|G, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|C, 7174_G|A,
7177_GG|AA, 7180_C|T, 7211_C|T, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7279_G|A, 7286_C|T, 7288_T|G, 7291_A|C, 7297_A|G,
7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7366_T|C, 7369_T|G, 7384_T|A, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C,
7423_C|T, 7426_CC|TT, 7429_A|G, 7432_T|C, 7441_C|T, 7450_A|G, 7453, 7459_.|Y, 7465_G|A, 7468_T|C, 7480_C|A, 7483_A|G, 7489_A|G, 7492_T|A, 7495_CT|TC, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G,
7519_C|T, 7528_T|C, 7531_T|G, 7552_C|G, 7561_A|G, 7571_A|C, 7579_TC|CT, 7582_C|T, 7588_T|C, 7597_A|T, 7612_A|C, 7624_A|T, 7630_A|G, 7634_C|A, 7642_C|A, 7645_G|A, 7651_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|A, 7753_G|A, 7762_G|A, 7765_T|C, 7771_C|T, 7789_C|T, 7798_G|T, 7804_C|G,
7807_G|A, 7813_C|T, 7816_A|T, 7819_GT|AC, 7825_G|A, 7831_C|T, 7837_G|A, 7851_A|G, 7861_T|C, 7869_T|C, 7876_G|A, 7879_G|A, 7882_T|C, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7918_A|G,
7921_G|A, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_T|C, 8011_C|T, 8014_C|T, 8023_A|G, 8041_A|G, 8044_A|G, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8086_A|G,
8089_AT|TC, 8092_G|A, 8095_A|G, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C, 8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_G|T, 8154_C|G, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8188_A|G,
8209_T|G, 8212_C|A, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8227_G|A, 8245_C|T, 8248_A|G, 8251_A|G, 8254_G|C, 8260_G|A, 8266_T|C, 8269_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T,
8299_C|T, 8302_G|A, 8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G, 8356_G|A, 8362_G|A, 8380_T|A, 8383_A|C, 8392_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A,
8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_ATGA|GCAG, 8510_T|A, 8512_T|C, 8518_TT|CC, 8533_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8574_A|G, 8584_A|G,
8587_T|C, 8590_G|A, 8593_G|A, 8596_C|T, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G, 8614_T|C, 8617_A|G, 8632_A|C, 8638_C|T, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8707_A|G, 8719_C|T, 8742_CG|TA,
8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8797_C|T, 8800_A|G, 8808_A|G, 8815_A|G, 8824_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|C,
8854_T|C, 8866_T|C, 8874_A|T, 8923_C|T, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8960_C|T, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8974_C|T, 8986_T|C, 9019_G|A, 9022_G|A, 9034_T|C, 9040_A|G,
9043_A|G, 9046_G|A, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9145_C|T, 9151_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9187_A|C, 9190_T|C, 9212_A|C, 9214_G|A, 9217_T|A, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9299_T|C, 9313_C|T, 9319_T|C,
9322_C|T, 9324_AA|GG, 9328_A|G, 9335_CAA|TTG, 9343_G|A, 9361_G|A, 9367_A|G, 9376_A|G, 9379_GT|CC, 9382_G|A, 9391_C|A, 9397_A|T, 9406_C|A, 9416_G|A, 9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G,
9445_C|T, 9467_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9505_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG, 9562_A|G, 9571_C|A, 9573_GG|AA,
9577_G|C, 9590_A|G, 9598_C|T, 9601_A|T, 9607_C|T, 9610_AC|GT, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9691_C|T, 9709_TA|GC, 9712_A|C, 9718_C|T,
9745_G|A, 9754_T|C, 9769_C|G, 9775_T|C, 9790_T|C, 9796_A|G, 9799_G|A, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9847_G|A, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T,
9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A, 9919_C|T, 9922_T|C, 9938_C|T, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10021_A|G,
10024_C|T, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10063_C|T, 10066_G|A, 10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10174_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10294_C|T, 10312_G|A, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10363_C|T, 10365_AA|TG, 10369_10377, 10383_10385,
10391_10394, 10396_10398, 10402_10407, 10409_10415, 10417_10418, 10422_A|C, 10425_C|T, 10427_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10464_10475, 10522, 10524_G|A,
10533_A|G, 10535_T|A, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_ACC|CTT, 10611_A|G, 10620_A|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10740_A|G, 10742_T|A, 10847_C|A

Case 3 (A.1): MH018100.1


Target: 835 samples Number of changes: 1407
BC: A.1.NmC2 + A.1 BC BR: 1383-1384 BC BR coord: 10152 - 10153
Direction L1: >> Initial region span: 1-1383,1402-1407Gap history (edge excluded): 1383-1402
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.72e-96 Rec. model vs L2: 1.65e-142
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1383 253.040540 NaN NaN NaN * * *
A.1.NmC1 0 3 0.251317 -1076.329321 5228.658642 0.000000e+00
A.1 835 4 0.102074 -105.023005 3286.046009 3.121378e-156
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1402 0.440912 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 217_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 444_A|C, 448_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 631_C|T,
649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 694_T|C, 700_C|T, 703_A|C, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1183_T|C, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A,
1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1726_A|G, 1729_C|A, 1738_A|G,
1741_A|T, 1744_T|C, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1951_A|G, 1957_C|A, 1960_C|T, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T,
2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2131_T|C, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G,
2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T,
2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2407_C|T, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C,
2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|T, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T,
2596_C|T, 2599_T|C, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2687_T|C, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2920_G|A, 2932_G|A, 2947_A|T, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3343_A|G, 3346_C|T, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3388_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3446_C|T, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G,
3514_A|G, 3517_A|C, 3523_T|A, 3529_T|C, 3535_T|A, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A,
3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3664_G|A, 3667_A|G, 3679_T|G, 3682_G|T, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3727_T|C, 3733_GT|CC, 3739_T|C,
3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C,
3895_T|A, 3898_T|C, 3901_C|A, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4396_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4429_G|A, 4435_G|A, 4438_G|A,
4441_T|C, 4453_A|G, 4465_C|T, 4471_T|C, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4510_T|C, 4519_T|A, 4522_TC|CT, 4525_G|A, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C,
4557_G|A, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|C, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4660_A|C, 4663_C|A,
4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4801_C|T, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G,
4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|C, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G,
5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C,
5269_T|C, 5284_G|A, 5287_T|C, 5297_C|T, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5332_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T,
5497_T|C, 5500_G|A, 5509_A|G, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5557_A|G, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G,
5656_C|T, 5662_A|C, 5668_C|T, 5674_A|C, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T,
5986_T|C, 5989_A|G, 6004_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6037_C|T, 6043_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6112_CG|TA, 6115_T|A,
6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A,
6286_G|A, 6310_C|T, 6313_T|C, 6316_A|G, 6322_G|A, 6334_T|C, 6346_A|C, 6352_G|A, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6427_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6532_C|G, 6547_C|T, 6550_T|C,
6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_CA|TG, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6860_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6943_A|G, 6958_TT|CG,
6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7036_C|T, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7177_G|T, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7441_C|T, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G,
7561_A|T, 7571_A|C, 7579_TC|CT, 7597_A|T, 7612_A|C, 7618_G|A, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7858_A|G, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7920_AG|GA,
7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7990_T|C, 7996_A|G, 8011_C|T, 8014_C|T, 8020_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G,
8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C,
8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8221_G|A, 8224_AT|GC, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8317_C|T, 8321_G|A, 8324_A|G, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A,
8518_TT|CC, 8524_CA|TG, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8569_C|T, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8605_T|C, 8608_T|G,
8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8788_C|T,
8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8950_A|G, 8954_A|C, 8956_GAA|ACG, 8965_C|T,
8968_A|G, 8971_A|G, 8980_T|C, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|T, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T,
9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C,
9324_AA|GG, 9328_AC|GT, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C,
9466_TC|CT, 9481_C|T, 9485_T|C, 9493_C|T, 9497_T|C, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|C, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9688_T|C, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC,
9745_G|A, 9749_A|G, 9754_T|C, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10047_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10154_G|A, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T,
10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10270_T|C, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10303_C|T

Case 3 (A.1): MH018101.1


Target: 835 samples Number of changes: 1412
BC: A.1.NmC2 + A.1 BC BR: 1388-1389 BC BR coord: 10152 - 10153
Direction L1: >> Initial region span: 1-1388,1407-1412Gap history (edge excluded): 1388-1407
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.72e-96 Rec. model vs L2: 2.88e-140
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1388 248.473717 NaN NaN NaN * * *
A.1.NmC1 0 3 0.251317 -1085.159657 5250.319314 0.000000e+00
A.1 835 4 0.102074 -104.354436 3288.708872 5.859735e-154
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1407 0.440912 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 217_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 444_A|C, 448_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 631_C|T,
649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 694_T|C, 700_C|T, 703_A|C, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1183_T|C, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1339_C|T, 1345_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1726_A|G, 1729_C|A,
1738_A|G, 1741_A|T, 1744_T|C, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1960_C|T, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2131_T|C, 2146_A|G, 2149_G|A,
2152_A|C, 2164_A|G, 2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2407_C|T, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|T, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A,
2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2687_T|C, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G,
2722_G|T, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T,
2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2920_G|A, 2932_G|A, 2947_A|T, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A,
3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3343_A|G, 3346_C|T, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3388_T|C,
3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3446_C|T, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3484_T|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_T|A, 3529_T|C, 3535_T|A, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C,
3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3664_G|A, 3667_A|G, 3679_T|G, 3682_G|T, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T,
3727_T|C, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A,
3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|A, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C,
4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4142_C|T,
4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4267_T|A, 4273_GA|AG,
4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4396_C|T, 4399_C|T, 4409_G|A,
4411_A|T, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4471_T|C, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4510_T|C, 4519_T|A, 4522_TC|CT, 4525_G|A,
4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4557_G|A, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|C, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C,
4645_T|C, 4654_C|T, 4660_A|C, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4756_G|A,
4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4801_C|T, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC,
4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|C, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T,
4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C,
5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5297_C|T, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5332_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5509_A|G, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5557_A|G, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5656_C|T, 5662_A|C, 5668_C|T, 5674_A|C, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6037_C|T, 6043_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6112_CG|TA, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6313_T|C, 6316_A|G, 6322_G|A, 6334_T|C, 6346_A|C, 6352_G|A, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6427_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG,
6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T,
6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6709_T|C, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G,
6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G,
6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7036_C|T,
7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A,
7177_G|T, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7441_C|T, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7561_A|T, 7571_A|C, 7579_TC|CT, 7597_A|T, 7612_A|C, 7618_G|A, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7768_G|A, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7858_A|G, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G,
7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7920_AG|GA, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7990_T|C, 7996_A|G, 8011_C|T,
8014_C|T, 8020_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A,
8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8221_G|A, 8224_AT|GC, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8317_C|T, 8321_G|A, 8324_A|G, 8326_A|G, 8329_T|C, 8338_C|T,
8354_C|T, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_CA|TG, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|T, 8574_A|G,
8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G,
8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8788_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8854_T|C, 8866_T|C, 8874_A|T, 8911_G|A, 8923_C|T,
8926_A|G, 8939_C|T, 8941_G|A, 8950_A|G, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|T,
9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T,
9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9324_AA|GG, 9328_AC|GT, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G,
9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9481_C|T, 9485_T|C, 9493_C|T, 9497_T|C, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|C, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9688_T|C, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10047_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G,
10148_A|C, 10154_G|A, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10270_T|C, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10303_C|T

Case 3 (A.1): MW158338.1


Target: 835 samples Number of changes: 1421
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 729-730, 1389-1390 BC BR coord: 5403 - 5404, 10381 - 10382
Direction L1: << Initial region span: 1-271,736-1389,1390-1421Gap history (edge excluded): 271-1390 -> 271-736
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.64e-48
Rec. model vs L1: 5.97e-84 Rec. model vs L2: 2.83e+23
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 271 20.872424 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 736 13.089629 NaN NaN NaN * * *
A.1.NmC2 0 1389 -10.000000 -96.518957 1911.037913 5.607385e-48
A.1.NmC1 0 1389 -10.000000 -1638.363688 4994.727375 0.000000e+00
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1390 24.431731 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 117_AC|GA, 130_T|C, 166_A|T, 226_C|T, 247_T|C, 260_A|G, 262_C|T, 271_T|C, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
332_C|T, 346_A|G, 363_GG|AC, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 433_TC|CT, 448_C|T, 451_A|G, 455_T|C, 464_C|T, 467_T|C, 473_A|G, 475_G|T,
488_T|C, 496_G|C, 514_C|T, 517_A|G, 523_G|C, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 613_A|G, 628_T|C, 631_C|T, 634_T|C, 637_C|T, 649_G|A,
655_A|T, 664_T|A, 676_C|T, 691_C|T, 694_T|C, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 757_C|T, 763_T|C, 766_G|A, 775_C|T, 784_G|A, 790_C|T, 802_A|G,
814_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 931_C|T, 934_G|C, 937_T|A, 961_T|C, 964_G|A,
970_C|T, 973_A|G, 985_T|A, 991_T|A, 1021_T|C, 1024_A|G, 1030_T|C, 1036_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1102_C|A, 1106_C|T, 1111_G|A, 1117_A|T,
1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1181_A|G, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1222_T|C, 1228_G|A, 1231_C|T, 1237_G|A,
1240_C|T, 1243_T|C, 1246_G|C, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1393_A|G, 1399_A|G, 1408_A|C, 1411_G|A,
1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1482_TC|CT, 1491_T|C, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1544_G|A,
1546_T|C, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1578_G|A, 1585_A|T, 1606_G|A, 1609_C|T, 1621_A|T, 1642_G|T, 1651_A|G, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1705_AC|GT,
1708_G|A, 1714_G|T, 1723_G|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1768_A|G, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_T|C, 1819_T|A, 1822_C|T, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CG, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G,
1954_A|G, 1957_C|A, 1969_T|C, 1978_A|G, 1981_A|C, 1993_T|C, 2002_AA|GG, 2008_T|C, 2011_A|G, 2020_G|A, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2041_C|T, 2044_A|C, 2050_T|C, 2063_C|T,
2080_A|T, 2083_T|C, 2089_A|G, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_TC|CT, 2128_C|G, 2131_T|C, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2176_T|C, 2188_A|G, 2193_TG|CA,
2201_C|T, 2209_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2302_G|A, 2305_GC|AT, 2308_A|G,
2314_C|T, 2322_A|G, 2341_C|T, 2349_C|T, 2353_A|T, 2356_T|C, 2380_A|G, 2401_C|T, 2408_T|C, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2452_G|T, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|T, 2488_G|A,
2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_T|C, 2515_A|T, 2524_C|T, 2527_T|A, 2533_C|T, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G,
2620_CC|TT, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2692_G|A, 2695_A|G, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT,
2737_TG|CA, 2740_T|C, 2752_A|G, 2755_T|A, 2773_T|C, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2803_T|C, 2809_T|C, 2812_G|A, 2818_T|C, 2827_C|T, 2833_G|A, 2836_G|A, 2878_A|G, 2881_C|T,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2914_G|A, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3001_CT|TC, 3019_C|T, 3034_C|A, 3040_C|G, 3043_T|C, 3064_T|C,
3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3104_G|A, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3247_C|T, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3319_CA|AG,
3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|C, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3412_T|A, 3421_C|T, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3457_T|C, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3481_C|T, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3508_T|C, 3514_A|G, 3517_A|T, 3523_T|A, 3529_T|C, 3535_T|G, 3556_A|C, 3569_C|T, 3571_A|G, 3577_A|G, 3589_A|C, 3598_G|A,
3604_T|C, 3610_AG|CA, 3613_A|G, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3646_A|G, 3649_TC|CA, 3652_CC|TT, 3655_T|G, 3658_T|C, 3662_C|T, 3667_A|G, 3679_TG|CA,
3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3742_T|C, 3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3763_G|A, 3772_C|T, 3782_C|T, 3784_C|A, 3790_C|G, 3793_A|G,
3802_T|C, 3814_T|C, 3824_C|T, 3826_A|G, 3829_A|G, 3832_A|C, 3851_T|C, 3860_G|A, 3868_C|G, 3872_C|T, 3883_T|C, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3910_G|A, 3928_T|C, 3934_G|A, 3947_AC|GT,
3950_A|G, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T,
4078_G|A, 4081_T|C, 4087_T|C, 4099_C|T, 4105_C|G, 4111_T|C, 4115_C|T, 4120_C|A, 4129_A|G, 4141_CC|TT, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4180_G|A, 4183_T|C, 4198_G|A, 4201_A|G,
4204_C|T, 4210_A|T, 4219_A|C, 4222_G|A, 4228_GC|CT, 4234_A|C, 4237_A|T, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|G, 4285_A|G, 4289_C|A, 4291_C|T,
4306_T|C, 4324_G|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4354_A|T, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4435_G|A,
4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4471_T|C, 4480_C|T, 4483_GC|AT, 4489_CT|TC, 4495_T|C, 4498_G|A, 4501_T|C, 4504_CC|TA, 4507_C|T, 4513_A|G, 4519_T|A, 4522_TC|CT, 4525_G|A, 4531_C|T,
4540_G|C, 4544_C|T, 4549_T|C, 4557_GG|AA, 4564_T|C, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|T, 4591_T|C, 4594_T|C, 4600_T|A, 4606_G|A, 4609_C|T, 4612_C|T, 4618_A|G, 4625_C|T, 4627_T|C, 4654_C|T,
4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4708_G|T, 4711_G|C, 4720_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|G,
4765_G|A, 4772_A|G, 4780_T|C, 4792_A|C, 4807_C|T, 4820_T|C, 4834_A|G, 4852_G|A, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4897_C|G, 4900_C|T, 4903_C|T, 4906_G|A, 4912_A|G, 4915_G|A,
4919_T|C, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4969_T|C, 4975_T|C, 4984_A|C, 4987_A|T, 4993_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T,
5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5110_G|A, 5113_C|G, 5116_A|G, 5119_G|A, 5122_C|T, 5143_A|G, 5153_G|A, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T,
5212_C|T, 5224_G|A, 5239_T|A, 5248_G|A, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5284_G|A, 5287_T|C, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5335_C|T, 5338_C|T,
5344_G|A, 5347_A|G, 5353_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5440_A|G, 5446_T|C, 5458_A|G,
5464_C|T, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5509_A|G, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5575_T|G, 5578_A|G, 5584_A|G, 5602_A|T, 5605_C|T, 5626_G|C, 5639_C|T,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5680_C|T, 5683_A|G, 5692_T|C, 5701_T|A, 5713_T|C, 5716_G|A, 5737_CC|GT, 5743_C|T, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C,
5800_A|T, 5821_A|G, 5836_T|C, 5839_C|T, 5846_C|A, 5854_G|A, 5860_C|T, 5872_T|C, 5875_G|A, 5878_T|G, 5884_T|C, 5917_G|A, 5923_T|C, 5926_T|C, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5962_C|T, 5968_G|A, 5971_A|G, 5974_T|C, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|T, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6055_C|T, 6065_T|C, 6067_G|A, 6097_C|T,
6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A,
6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|G, 6352_G|A, 6358_G|A, 6361_C|T, 6373_T|C, 6388_A|G, 6400_T|C,
6406_GT|TG, 6412_A|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G, 6439_G|A, 6442_A|G, 6451_A|G, 6457_A|G, 6478_T|A, 6481_T|C, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6527_T|C,
6530_C|T, 6532_C|G, 6550_T|C, 6569_C|T, 6583_T|C, 6597_T|C, 6599_G|A, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6634_G|T, 6637_A|G, 6643_C|T, 6658_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6733_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6850_T|C, 6859_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6883_A|G, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6934_G|A,
6940_CT|TG, 6943_A|G, 6952_T|C, 6956_G|A, 6958_TT|CG, 6970_T|C, 6976_G|A, 6979_TC|CT, 6991_G|A, 6994_A|G, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C,
7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7084_TC|CT, 7096_A|C, 7114_CC|TT, 7117_T|G, 7120_T|A, 7123_C|T, 7135_G|T, 7138_A|T, 7141_A|G, 7149_A|G, 7156_T|C, 7171_G|T, 7174_G|A,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7252_C|T, 7256_T|C, 7258_A|G, 7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|A, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_CC|TT, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7435_T|C, 7438_T|C, 7447_C|T, 7450_A|G, 7453_G|A, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7495_CT|TC, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7555_C|T, 7571_A|C, 7579_TC|CT, 7597_A|T, 7612_A|C, 7624_AA|GT, 7630_A|G, 7634_C|A, 7651_A|G, 7654_A|G, 7658_T|C, 7663_T|C,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_G|A, 7712_T|C, 7726_C|A, 7738_G|A, 7750_T|G, 7753_G|A, 7756_A|T, 7759_CA|TC, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T,
7792_G|A, 7798_G|T, 7801_C|G, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7861_T|A, 7869_T|C, 7876_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A,
7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7942_A|T, 7948_T|C, 7951_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7990_T|C, 7996_A|G, 8011_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8053_A|G, 8065_T|A, 8071_T|C, 8080_A|G, 8089_AT|TC, 8098_G|A, 8101_C|G, 8104_A|T, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|T, 8167_C|A, 8169_A|G,
8173_C|T, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8269_C|T, 8275_G|A, 8278_T|C, 8281_C|A, 8284_T|C, 8290_A|G, 8296_C|T, 8320_TG|CA,
8326_A|G, 8329_T|C, 8344_A|G, 8356_G|A, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|C, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8452_C|A, 8455_G|T, 8458_C|A, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_C|T, 8505_.|C, 8507, 8510_T|A, 8518_T|C, 8533_C|T, 8551_C|T, 8557_T|C, 8563_C|T, 8574_A|G, 8578_C|T, 8584_A|G, 8587_T|C,
8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8741_G|A,
8743_G|A, 8746_A|G, 8749_T|G, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|C, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8854_T|C, 8866_T|C, 8874_A|T, 8884_A|G,
8905_C|T, 8911_G|A, 8914_T|C, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8941_G|A, 8950_A|G, 8954_A|C, 8956_GAA|ACG, 8968_A|G, 8971_A|G, 8998_C|T, 9010_A|G, 9019_G|A, 9022_G|A, 9037_G|A,
9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9104_C|T, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T,
9184_A|G, 9187_A|C, 9190_T|C, 9199_A|G, 9202_C|T, 9212_A|C, 9214_G|A, 9217_T|A, 9229_C|T, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_GA|AG, 9299_T|C,
9307_C|T, 9313_C|T, 9319_T|C, 9324_A|G, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9361_G|A, 9364_C|T, 9367_A|G, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|A, 9424_T|C, 9430_A|G,
9445_C|T, 9454_A|G, 9457_G|A, 9460_T|C, 9466_TC|CT, 9472_C|T, 9481_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA,
9562_A|G, 9565_TC|CT, 9569_A|G, 9573_GG|AA, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C, 9607_C|T, 9610_A|G, 9613_G|A, 9625_G|A, 9637_C|T, 9646_G|T, 9649_C|T, 9658_C|T, 9673_C|T, 9703_C|T,
9709_TA|AC, 9745_G|A, 9749_A|G, 9754_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9796_A|G, 9799_G|A, 9817_G|A, 9820_T|C, 9829_T|C, 9835_A|G, 9838_A|T, 9844_C|T, 9850_C|A, 9865_G|A, 9880_C|T, 9883_C|T,
9895_G|A, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9938_C|T, 9946_T|C, 9949_T|C, 9955_A|G, 9970_AC|GT, 9973_G|A, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10066_G|A, 10072_C|T, 10096_A|G, 10103_A|G, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10156_C|T, 10159_T|C, 10162_T|C,
10165_A|G, 10180_C|T, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10259_C|A, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10291_C|T, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10312_G|A, 10315_T|C, 10331_C|T, 10336_A|G, 10338_TG|CT, 10348_T|C, 10351_C|T, 10355_A|G,
10361_A|G, 10363_10372, 10374_10375, 10378_G|A, 10382, 10385, 10391_10397, 10403_C|T, 10406_10415, 10420_10429, 10431_A|G, 10434_10436, 10439_10442, 10444_10445, 10450_10463, 10470_10474,
10475_A|T, 10522, 10524_G|A, 10533_A|T, 10535_T|A, 10549_C|T, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10635_G|A, 10639_C|T, 10647_C|T, 10657_.|C, 10659_G|A,
10681_CT|TC, 10739_A|T, 10742_T|C

Case 3 (A.1): MW158339.1


Target: 835 samples Number of changes: 1432
BC: A.1.NmC2 + A.1 BC BR: 3-4 BC BR coord: 129 - 130
Direction L1: << Initial region span: 1-3,4-1432Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.36e-04
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 3 5.083407 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 4 38.911599 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 130_T|C, 166_A|T, 226_C|T, 247_T|C, 260_262, 263_T|G, 272_.|TCT, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_AA|GG,
332_C|T, 346_A|G, 363_GG|AC, 367_A|G, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 433_TC|CT, 448_C|T, 451_A|G, 455_T|C, 464_C|T, 467_T|C, 473_A|G, 475_G|T, 488_T|C,
496_G|C, 514_C|T, 517_A|G, 523_G|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 613_A|G, 628_T|C, 631_C|T, 634_T|C, 637_C|T, 649_G|A, 655_A|T, 664_T|A,
676_C|T, 682_G|A, 691_C|T, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 757_C|T, 763_T|C, 766_G|A, 772_A|G, 775_C|T, 781_T|C, 784_G|A, 790_C|T, 802_A|G,
814_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 841_G|A, 844_T|C, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 874_T|C, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 931_C|T, 934_G|C, 937_T|A,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 1021_T|C, 1024_A|G, 1030_T|C, 1036_T|C, 1040_G|A, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1102_C|A,
1106_C|T, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1150_G|A, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1222_T|C,
1228_G|A, 1231_C|T, 1237_G|A, 1240_C|T, 1243_T|C, 1246_G|T, 1255_C|G, 1261_T|C, 1279_C|A, 1294_A|G, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1393_A|G, 1399_AT|GC,
1405_T|C, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1482_TC|CT, 1491_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C,
1534_G|A, 1544_G|A, 1546_T|C, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1578_G|A, 1585_A|T, 1591_C|T, 1606_G|A, 1609_C|T, 1621_A|T, 1642_G|T, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T,
1693_C|A, 1705_AC|GT, 1708_G|A, 1711_C|T, 1714_G|T, 1723_G|A, 1733_T|C, 1738_A|G, 1741_A|T, 1744_T|C, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1768_A|G, 1771_G|A, 1780_TG|CA, 1785_A|G,
1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C, 1819_T|A, 1822_C|T, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C,
1894_C|T, 1900_C|T, 1915_C|A, 1926_TT|CG, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1969_T|C, 1978_A|G, 1981_A|C, 1993_T|C, 2002_AA|GG, 2008_T|C, 2011_A|G, 2020_G|A, 2023_T|C,
2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2050_T|C, 2063_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2095_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_TC|CT, 2128_C|G, 2131_T|C,
2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2176_T|C, 2188_A|G, 2193_TG|CA, 2201_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|T, 2230_T|C, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C,
2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2320_G|A, 2322_A|G, 2338_C|T, 2341_C|T, 2349_C|T, 2353_A|T, 2380_A|G, 2401_C|T, 2408_T|C, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2452_G|T, 2455_T|C, 2461_A|C, 2464_C|T, 2467_C|A, 2470_C|T, 2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_T|C, 2515_A|T, 2524_C|T, 2527_T|A, 2533_C|T, 2548_C|T,
2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2620_CC|TT, 2623_A|G, 2626_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2692_G|A, 2695_A|G,
2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2738_G|A, 2740_T|C, 2752_A|G, 2755_T|A, 2773_T|C, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2803_T|C,
2809_T|C, 2812_G|A, 2818_T|C, 2827_C|T, 2833_G|A, 2836_G|A, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2914_G|A, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3010_A|G, 3019_C|T, 3034_C|A, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3104_G|A, 3109_A|G,
3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|C, 3238_T|C, 3244_G|A, 3247_C|T, 3253_T|C,
3265_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|C, 3361_T|C, 3370_AG|GA, 3373_T|C,
3397_C|A, 3412_T|A, 3421_C|T, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3481_C|T, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3508_T|C,
3514_A|G, 3517_A|C, 3523_T|A, 3529_T|C, 3535_T|G, 3556_A|C, 3569_C|T, 3571_A|G, 3577_A|G, 3589_A|C, 3598_G|A, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T,
3634_G|A, 3637_C|T, 3640_G|A, 3646_A|G, 3649_TC|CA, 3652_CC|TT, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|C, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C,
3742_T|C, 3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3763_G|A, 3772_C|T, 3775_C|T, 3782_C|T, 3784_C|A, 3790_C|G, 3793_A|G, 3814_T|C, 3824_C|T, 3826_A|G, 3829_A|G, 3832_A|C, 3851_T|C, 3860_G|A,
3868_C|G, 3872_C|T, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3910_G|A, 3928_T|C, 3934_G|A, 3947_AC|GT, 3950_A|G, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|G, 4006_CG|AA, 4013_T|C,
4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4034_A|G, 4036_A|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4069_C|T, 4078_G|A, 4081_T|C, 4087_T|C, 4105_C|G, 4115_C|T,
4120_CT|AC, 4129_A|G, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4222_G|A, 4228_GC|CT, 4234_A|C, 4237_AC|TT, 4246_T|C,
4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|G, 4285_A|G, 4289_C|A, 4291_C|T, 4306_T|C, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4354_A|T, 4360_A|C, 4375_G|T, 4384_C|T,
4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4449_A|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4489_CT|TC, 4495_T|C, 4498_G|A,
4501_T|C, 4504_CC|TA, 4507_C|T, 4513_A|G, 4519_T|A, 4522_TC|CT, 4525_G|A, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4557_GG|AA, 4564_T|C, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|T, 4591_T|C,
4594_T|C, 4600_T|A, 4606_G|A, 4609_C|T, 4612_C|T, 4618_A|G, 4625_C|T, 4627_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4675_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4708_G|T, 4711_G|C,
4720_A|G, 4741_A|G, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|G, 4765_G|A, 4769_T|C, 4772_A|G, 4774_T|C, 4780_T|C, 4792_A|C, 4820_T|C, 4834_A|G, 4852_G|A, 4861_C|T, 4870_C|A,
4873_G|A, 4878_TT|CC, 4882_A|C, 4897_C|G, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4924_C|T, 4927_A|G, 4930_G|T, 4939_G|A, 4951_G|A, 4954_T|G, 4957_C|T, 4969_T|C, 4975_T|C, 4984_A|C,
4987_A|T, 4993_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5062_C|T, 5065_G|A, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5104_G|A, 5110_G|A, 5113_C|G, 5116_A|G,
5119_G|A, 5122_C|T, 5143_A|G, 5153_G|A, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5212_C|T, 5224_G|A, 5239_T|A, 5248_G|A, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5284_G|A, 5287_T|C,
5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5335_C|T, 5344_G|A, 5347_A|G, 5353_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5407_G|A, 5410_T|G,
5413_T|C, 5416_C|T, 5431_T|C, 5440_A|G, 5446_T|C, 5452_G|A, 5458_A|G, 5464_C|T, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5509_A|G, 5530_A|T, 5539_G|T, 5542_T|A,
5545_G|A, 5557_A|G, 5560_T|C, 5575_T|G, 5578_A|G, 5584_A|G, 5602_A|C, 5605_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5692_T|C, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5743_C|T, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|T, 5821_A|G, 5836_T|C, 5839_C|T, 5846_C|A, 5854_G|A, 5860_C|T, 5872_T|C, 5875_G|A, 5878_T|G,
5884_T|C, 5917_G|A, 5923_T|C, 5926_T|C, 5932_C|A, 5935_A|T, 5941_T|A, 5947_T|C, 5962_C|T, 5968_G|A, 5971_A|G, 5974_T|C, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|T,
6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6142_T|A, 6154_A|G, 6157_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C,
6211_C|T, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|G, 6352_G|A,
6358_G|A, 6361_C|T, 6373_T|C, 6388_A|G, 6400_T|C, 6406_GT|TG, 6412_A|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G, 6439_G|A, 6442_A|G, 6451_A|G, 6457_A|G, 6478_T|A, 6481_T|C, 6490_T|C, 6493_A|G,
6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6550_T|C, 6569_C|T, 6583_T|C, 6597_T|C, 6599_G|A, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6637_A|G,
6646_C|T, 6658_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6733_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6775_T|C, 6779_C|T,
6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6850_T|C, 6859_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6883_A|G, 6886_C|T,
6889_C|T, 6892_G|A, 6907_G|A, 6909_AA|GG, 6916_A|G, 6934_G|A, 6940_CT|TG, 6943_A|G, 6952_T|C, 6956_G|A, 6958_TT|CA, 6970_T|C, 6976_G|A, 6979_TC|CT, 6991_G|A, 6994_A|G, 7000_T|C, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|C, 7114_CC|TT, 7117_T|G, 7120_T|A, 7123_C|T, 7135_G|T, 7138_A|T,
7141_A|G, 7149_A|G, 7156_T|C, 7171_G|T, 7174_G|A, 7210_T|C, 7216_C|T, 7222_C|A, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7252_C|T, 7255_TT|CC, 7258_A|G, 7267_C|T, 7288_T|G, 7297_A|G,
7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|A, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_CC|TT, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7435_T|C,
7438_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|C, 7492_T|A, 7495_CT|TC, 7498_A|G, 7527, 7531_.|G, 7552_C|G, 7561_A|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7608_A|G, 7612_A|C,
7624_A|G, 7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7658_T|C, 7663_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7699_G|A, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7738_G|A, 7750_T|G,
7753_G|A, 7756_A|T, 7759_CA|TC, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7801_C|A, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7861_T|A, 7864_G|A,
7876_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7942_A|T, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7990_T|C,
7996_A|G, 8011_C|T, 8014_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_T|A, 8071_T|C, 8080_A|G, 8086_A|G, 8089_AT|TC, 8098_G|A, 8101_C|G, 8104_A|T, 8107_G|A, 8113_A|G,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8154_CT|GC, 8161_G|T, 8167_C|A, 8169_A|G, 8173_C|T, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|C,
8263_C|T, 8269_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8320_TG|CA, 8326_A|G, 8344_A|G, 8350_C|A, 8356_G|A, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|C, 8398_G|A, 8401_T|C,
8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8452_C|A, 8455_G|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_C|T, 8505_.|C, 8507, 8510_T|A, 8518_T|C,
8533_C|T, 8551_C|T, 8563_C|T, 8574_A|G, 8578_C|T, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A,
8656_A|G, 8671_T|A, 8677_A|G, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8741_G|A, 8743_G|A, 8746_A|G, 8749_T|G, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|C, 8788_C|T, 8792_C|T, 8815_A|G, 8830_A|G,
8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8854_T|C, 8857_T|C, 8866_T|C, 8874_A|T, 8884_A|G, 8905_C|T, 8911_G|A, 8914_T|C, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC,
8956_GAA|ACG, 8968_A|G, 8971_A|G, 9010_A|G, 9019_G|A, 9022_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9097_T|C, 9112_C|T, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9194_A|C, 9199_A|G, 9202_C|T, 9212_A|C, 9214_G|A, 9217_T|A, 9229_C|T, 9232_C|T, 9235_G|A,
9244_C|A, 9259_G|A, 9263_A|G, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_GA|AG, 9299_T|C, 9304_C|T, 9307_C|T, 9313_C|T, 9319_T|C, 9324_A|G, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG,
9361_G|A, 9364_C|T, 9367_A|G, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|A, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9457_G|A, 9460_T|C, 9466_T|C, 9472_C|T, 9481_C|T, 9485_T|C,
9490_A|G, 9497_T|C, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9565_TC|CT, 9569_A|G, 9573_GG|AA, 9577_G|C, 9590_A|G, 9598_C|T, 9601_A|C,
9607_C|T, 9610_A|G, 9625_G|A, 9637_C|T, 9643_T|C, 9646_G|T, 9649_C|T, 9658_C|T, 9679_C|T, 9703_C|T, 9709_TA|AC, 9745_G|A, 9749_A|G, 9754_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9787_C|T, 9796_A|G,
9799_G|A, 9802_G|A, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9844_C|T, 9850_C|A, 9865_G|A, 9880_C|T, 9895_G|A, 9898_A|G, 9904_T|G, 9910_C|T, 9916_A|G, 9922_T|C, 9938_C|T, 9946_T|C, 9949_T|C,
9955_A|G, 9970_AC|GT, 9973_G|A, 9977_T|C, 9985_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10072_C|T, 10096_A|G, 10103_A|G,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10156_C|T, 10159_T|C, 10162_T|C, 10165_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T,
10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10259_C|A, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10291_C|T, 10294_C|T, 10297_A|G, 10312_G|A,
10315_T|C, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_10369, 10371_10372, 10374_10381, 10383_10387, 10390_10397, 10402_10412, 10419_10421, 10424_10427, 10430_10440,
10447_10450, 10452_10454, 10457, 10458_C|T, 10460_C|T, 10463_T|A, 10466_A|G, 10470_G|A, 10475_A|T, 10522, 10524_G|A, 10533_A|T, 10535_T|G, 10549_C|T, 10555_AC|GT, 10558_A|G, 10562_T|C,
10605_A|C, 10607_C|T, 10635_G|A, 10647_C|T, 10658_.|C, 10659_AG|TA, 10681_CT|TC, 10742_T|C, 10783_C|T, 10785_C|G, 10788_C|T, 10794_C|A, 10799_G|A

Case 3 (A.1): MW158343.1


Target: 835 samples Number of changes: 1464
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 357-358, 1438-1439 BC BR coord: 2637 - 2638, 10430 - 10431
Direction L1: >> Initial region span: 1-357,358-363,1439-1464Gap history (edge excluded): 357-1439 -> 363-1439
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.21e-48
Rec. model vs L1: 5.24e-134 Rec. model vs L2: 4.76e-08
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 357 25.233308 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 363 0.817234 NaN NaN NaN * * *
A.1.NmC2 0 395 -2.104146 -170.131497 2864.262995 2.223504e-48
A.1.NmC1 0 360 -9.862128 -1395.366958 5314.733916 0.000000e+00
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1439 18.643849 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|A, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 448_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 496_G|C, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 532_G|A, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 628_T|C,
631_C|T, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCCAGAAG, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
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8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8324_A|G, 8326_A|G, 8329_T|C, 8338_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8407_CA|TG, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A,
8494_A|G, 8500_G|A, 8505_TGA|CCG, 8509_CT|TA, 8518_TT|CC, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C, 8569_C|T, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A,
8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8734_T|C, 8743_G|A, 8746_A|G, 8749_T|C,
8755_G|A, 8764_A|G, 8773_C|T, 8788_C|T, 8792_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8848_C|T, 8851_A|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8929_G|A,
8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8989_T|C, 9009_9010, 9017_.|AA, 9022_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9052_C|T, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9100_G|A, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9173_T|C, 9181_C|T, 9187_A|T, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9229_C|T, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9280_T|G, 9295_GA|AG, 9298_C|T, 9313_C|T, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9460_T|C, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G,
9497_T|C, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_GG|AA, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9607_C|T, 9610_A|G, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9766_G|A, 9769_C|T,
9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9865_G|A, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C,
9938_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|G, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G,
10111_C|T, 10128_AG|GA, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A,
10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10309_C|T,
10315_T|C, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_AT|GG, 10364_10365, 10366_A|C, 10369_G|A, 10378_G|A, 10382_10389, 10392_10394, 10399_10402, 10404_10406, 10409_10418,
10421_10431, 10434_10436, 10439_10442, 10444_10445, 10450_10463, 10466_10470, 10475_A|T, 10520, 10522_G|C, 10524_G|A, 10533_A|G, 10535_T|G, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G,
10562_T|C, 10568_C|T, 10605_A|C, 10607_C|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10662_C|T, 10681_CT|TC

Case 3 (A.1): MW158345.1


Target: 835 samples Number of changes: 1464
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 1427-1428, 1443-1444 BC BR coord: 10360 - 10361, 10468 - 10469
Direction L1: >> Initial region span: 1-1427,1428-1443,1444-1464Gap history (edge excluded): 1427-1444 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.20e-75
Rec. model vs L1: 2.72e-141 Rec. model vs L2: 3.06e-92
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1427 150.578078 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1443 3.123235 NaN NaN NaN * * *
A.1.NmC2 0 1428 -10.000000 -167.354496 398.708993 9.151172e-75
A.1.NmC1 0 1428 -10.000000 -160.000000 384.000000 1.431241e-71
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1444 26.880177 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 245_G|A, 247_T|C, 260_A|G, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 319_GT|AC, 322_G|A, 327_A|G,
340_A|G, 346_A|G, 352_G|A, 355_T|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 439_T|C, 448_C|T, 451_A|G,
455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T,
604_C|T, 610_C|T, 613_A|C, 628_T|C, 631_C|T, 640_T|C, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C,
760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 811_T|C, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|G, 879_TG|CA, 883_G|A,
886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1036_T|C,
1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT,
1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G,
1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C,
1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A,
1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT,
1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G,
1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A,
1926_TT|CA, 1930_G|A, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1963_C|T, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2023_T|C, 2029_T|C, 2032_C|T,
2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2086_T|C, 2089_A|G, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A,
2152_A|C, 2164_A|G, 2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2401_C|T, 2408_T|C, 2410_G|A,
2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2491_C|T, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2554_C|T,
2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2602_T|C, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T,
2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|A, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C,
3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G,
3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3446_C|T, 3448_C|T, 3454_A|G, 3460_G|A,
3466_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G,
3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
3672_C|T, 3679_T|G, 3682_G|T, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3814_T|C, 3826_A|T,
3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G,
3971_T|C, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|T, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
4099_C|T, 4105_C|G, 4117_G|A, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CT, 4165_C|A, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT,
4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4289_C|A, 4301_C|T, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C,
4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|A, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C,
4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C,
4720_A|G, 4729_T|C, 4735_AA|TC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T,
4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T,
5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T,
5200_A|C, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5297_C|T, 5299_G|A, 5302_C|T, 5305_G|C,
5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C,
5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5494_A|G, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A,
5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5653_G|A, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A,
5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_AT|CC, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T,
5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5956_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6160_G|A, 6174_AA|GG, 6182_A|C, 6187_A|G,
6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6378_A|C, 6388_A|G, 6406_GT|TG, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T,
6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6661_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T,
6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A,
6874_A|T, 6876_CG|TA, 6889_C|T, 6892_GC|AT, 6898_C|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6956_G|T, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A,
6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7042_A|T, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|A, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_G|A, 7180_C|T, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_T|C, 7258_A|G,
7261_T|C, 7267_C|T, 7288_T|G, 7294_G|A, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7354_C|T, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_CC|GT, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C,
7579_TC|CT, 7597_A|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C,
7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7780_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A,
7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7874_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7948_T|C, 7956_GA|AG,
7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7996_A|G, 8011_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A,
8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8221_G|A,
8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8324_A|G, 8326_A|G, 8329_T|C,
8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T,
8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|C, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8557_T|C,
8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C,
8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 9009_9010, 9017_.|AA, 9022_G|A,
9037_G|A, 9040_A|G, 9061_A|C, 9067_T|C, 9082_G|T, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C,
9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9289_A|G, 9295_G|A, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9775_T|C, 9787_C|T,
9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|C, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C,
9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T,
10132_AA|GG, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T,
10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_10369, 10371_10372, 10374_10381, 10383_10387, 10391_10397, 10401_10412, 10419_10421, 10424_10427, 10430_10437, 10439_10441,
10444_10445, 10449_10454, 10457_CC|TT, 10460_C|T, 10463_T|A, 10466_A|G, 10475_A|T, 10520, 10522_G|C, 10524_G|A, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C,
10605_A|C, 10607_C|T, 10612_G|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10662_C|T, 10681_CT|TC

Case 3 (A.1): MW158346.1


Target: 835 samples Number of changes: 1460
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 1425-1426, 1441-1442 BC BR coord: 10360 - 10361, 10468 - 10469
Direction L1: >> Initial region span: 1-1425,1426-1441,1442-1460Gap history (edge excluded): 1425-1442 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.15e-75
Rec. model vs L1: 2.72e-141 Rec. model vs L2: 1.34e-101
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1425 170.578078 NaN NaN NaN * * *
A.1.NmC1 0 19 -0.893774 -1217.933572 5629.867144 0.0
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1441 3.123235 NaN NaN NaN * * *
A.1.NmC2 0 1426 -10.000000 -167.354496 398.708993 9.151172e-75
A.1.NmC1 0 1426 -10.000000 -160.000000 384.000000 1.431241e-71
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1442 23.471782 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 319_GT|AC, 322_G|A, 327_A|G, 340_A|G,
346_A|G, 352_G|A, 355_T|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 439_T|C, 448_C|T, 451_A|G, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T,
610_C|T, 613_A|C, 628_T|C, 631_C|T, 640_T|C, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A,
763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 811_T|C, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|G, 879_TG|CA, 883_G|A,
886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1036_T|C,
1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT,
1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G,
1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C,
1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A,
1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT,
1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G,
1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A,
1926_TT|CA, 1930_G|A, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1963_C|T, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2023_T|C, 2029_T|C, 2032_C|T,
2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2086_T|C, 2089_A|G, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A,
2152_A|C, 2164_A|G, 2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2401_C|T, 2408_T|C, 2410_G|A,
2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2491_C|T, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2554_C|T,
2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2602_T|C, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G,
2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T,
2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|A, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C,
3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G,
3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3446_C|T, 3448_C|T, 3454_A|G, 3460_G|A,
3466_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G,
3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G,
3672_C|T, 3679_T|G, 3682_G|T, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3814_T|C, 3826_A|T,
3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G,
3971_T|C, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|T, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
4099_C|T, 4105_C|G, 4117_G|A, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CT, 4165_C|A, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT,
4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4289_C|A, 4301_C|T, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C,
4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|A, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C,
4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C,
4720_A|G, 4729_T|C, 4735_AA|TC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T,
4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T,
5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T,
5200_A|C, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5297_C|T, 5299_G|A, 5302_C|T, 5305_G|C,
5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C,
5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5494_A|G, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A,
5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5653_G|A, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A,
5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_AT|CC, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T,
5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5956_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T,
6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6160_G|A, 6174_AA|GG, 6182_A|C, 6187_A|G,
6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C,
6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C,
6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6527_T|C, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6661_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA,
6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T,
6876_CG|TA, 6889_C|T, 6892_GC|AT, 6898_C|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6956_G|T, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT,
6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7042_A|T, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|A, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT,
7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_G|A, 7180_C|T, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_T|C, 7258_A|G, 7261_T|C,
7267_C|T, 7288_T|G, 7294_G|A, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7354_C|T, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G,
7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_CC|GT, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT,
7597_A|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A,
7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7780_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A,
7864_G|A, 7869_T|C, 7874_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C,
7969_G|A, 7972_A|G, 7996_A|G, 8011_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C,
8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8324_A|G, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG,
8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|C, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8566_T|C,
8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A,
8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 9009_9010, 9017_.|AA, 9022_G|A, 9037_G|A, 9040_A|G,
9061_A|C, 9067_T|C, 9082_G|T, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C,
9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9289_A|G, 9295_G|A, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T,
9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C,
9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9775_T|C, 9787_C|T, 9796_A|G, 9799_G|A,
9817_G|A, 9823_G|A, 9835_A|G, 9838_A|C, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10132_AA|GG, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G,
10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C,
10351_C|T, 10355_A|G, 10361_10369, 10371_10372, 10374_10381, 10383_10387, 10391_10397, 10401_10412, 10419_10421, 10424_10427, 10430_10437, 10439_10441, 10444_10445, 10449_10454, 10457_CC|TT,
10460_C|T, 10463_T|A, 10466_A|G, 10475_A|T, 10520, 10522_G|C, 10524_G|A, 10533_A|G, 10535_T|A, 10549_C|A, 10553_A|G, 10555_AC|GT, 10558_A|G, 10562_T|C, 10605_ACC|CTT, 10635_G|A, 10639_C|T,
10647_C|T, 10653_.|G, 10657_AAG|CCA, 10662_C|T, 10681_CT|TC

Case 3 (A.1): MW158359.1


Target: 835 samples Number of changes: 1480
BC: A.1 + A.1 BC BR: 1458-1459 BC BR coord: 10443 - 10444
Direction L1: >> Initial region span: 1-1437,1467-1480Gap history (edge excluded): 1437-1467
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.32e-12
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1437 210.12314 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1467 1.281111 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 178_T|C, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C, 327_AA|GG,
340_A|G, 346_A|G, 349_C|A, 352_G|A, 361_A|G, 363_G|A, 367_A|G, 376_A|G, 385_C|G, 389_T|C, 400_A|C, 409_A|G, 418_C|T, 421_T|A, 430_T|A, 433_T|C, 442_G|T, 448_C|T, 451_A|G, 454_TT|CC, 457_G|A,
467_T|C, 475_G|T, 496_G|T, 499_A|G, 501_A|G, 514_CC|TT, 517_A|G, 523_G|T, 529_T|C, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 594_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T,
613_A|C, 628_T|C, 634_T|C, 637_CA|TG, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|G, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 745_A|G,
754_T|C, 757_C|T, 760_G|A, 763_T|C, 766_G|A, 790_C|T, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|T, 883_G|A, 887_C|T, 889_GA|AG,
901_CC|TT, 904_T|A, 910_A|G, 931_C|T, 940_CC|TT, 943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 997_C|T, 1036_T|C, 1042_T|C, 1045_C|T, 1051_G|A, 1054_A|G,
1066_C|T, 1072_T|G, 1090_T|C, 1094_T|C, 1102_C|A, 1106_C|T, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1181_A|G, 1183_T|A,
1189_C|T, 1204_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT, 1219_A|G, 1222_T|C, 1228_G|A, 1234_A|G, 1237_G|A, 1240_C|T, 1243_T|C, 1246_G|C, 1252_G|A, 1255_C|G, 1258_T|C, 1261_T|C, 1279_C|G, 1285_C|T,
1294_A|G, 1300_G|A, 1306_G|A, 1327_A|G, 1330_C|T, 1333_T|C, 1342_A|G, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1400_T|C, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1433_A|G, 1435_C|T,
1447_T|C, 1453_G|A, 1471_C|T, 1474_C|T, 1480_A|G, 1482_TC|CT, 1486_G|A, 1489_C|T, 1491_T|C, 1495_G|A, 1501_A|G, 1504_A|G, 1507_T|C, 1511_C|T, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1534_G|A,
1544_G|A, 1546_T|C, 1552_T|C, 1561_T|A, 1570_A|G, 1572_C|G, 1585_A|T, 1591_C|T, 1603_C|T, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T,
1693_C|A, 1701_G|A, 1705_AC|GT, 1712_C|T, 1720_C|T, 1723_G|A, 1732_C|T, 1738_A|G, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1771_G|A, 1782_A|G, 1785_AC|GT, 1792_T|G, 1798_A|G, 1801_A|G,
1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C, 1819_T|A, 1822_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1876_T|C, 1887_T|C, 1894_C|T, 1900_C|T, 1912_T|A, 1915_C|A, 1926_TT|CC, 1930_G|A, 1946_T|C, 1978_A|G,
1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C, 2017_T|C, 2023_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2053_T|A, 2059_A|G, 2063_C|T, 2080_A|C, 2083_T|C, 2086_T|C, 2089_A|G, 2104_C|A,
2112_G|C, 2116_A|G, 2119_T|C, 2125_T|A, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2191_C|T, 2193_T|C, 2197_A|G, 2201_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|T,
2230_T|C, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2266_G|A, 2275_T|A, 2278_T|C, 2280_C|T, 2290_C|T, 2302_G|A, 2305_GC|AT, 2308_A|G, 2322_A|G, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G,
2407_CT|TC, 2413_A|T, 2419_G|C, 2432_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2467_C|A, 2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2515_A|T, 2518_T|C, 2521_A|G, 2524_C|T,
2527_T|A, 2533_C|T, 2548_C|T, 2566_T|C, 2569_T|G, 2581_A|T, 2593_A|G, 2599_T|C, 2605_A|G, 2621_C|T, 2626_T|C, 2632_T|C, 2638_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2662_C|T, 2665_G|A,
2668_A|G, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_T|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2755_T|A, 2761_A|T, 2776_G|T,
2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2812_G|A, 2814_A|G, 2824_C|T, 2827_C|T, 2833_G|A, 2836_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2923_G|A, 2926_T|C, 2947_A|T, 2950_C|A, 2962_C|T, 2968_C|T, 2980_C|A, 2983_A|G, 3007_T|G, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3142_T|C, 3169_TG|CA, 3172_A|C, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3223_C|T, 3226_T|A, 3238_T|C,
3243_CG|TA, 3247_C|T, 3250_A|G, 3265_A|G, 3271_A|G, 3289_T|C, 3292_C|T, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|TGG, 3331_A|G, 3334_G|T, 3343_A|T, 3349_A|G,
3358_G|C, 3361_T|C, 3364_C|T, 3370_AG|GA, 3373_T|C, 3394_C|A, 3397_C|A, 3400_C|T, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3457_T|C, 3460_G|A, 3469_A|C, 3472_G|A,
3480_G|A, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3514_AA|GG, 3517_A|C, 3523_TG|AA, 3535_T|G, 3569_C|T, 3571_A|G, 3573_G|A, 3577_A|G, 3583_G|A, 3589_A|C, 3598_GT|AC, 3610_A|C, 3620_T|C,
3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|C, 3649_T|C, 3652_CC|GT, 3655_T|A, 3667_A|G, 3670_C|A, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T,
3727_T|C, 3733_GT|TC, 3739_T|C, 3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3760_A|G, 3763_G|A, 3772_C|T, 3778_T|C, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3802_T|C, 3805_G|A, 3820_G|A, 3826_A|G,
3832_A|T, 3847_T|A, 3856_T|C, 3860_G|A, 3868_C|A, 3871_C|G, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3939_C|T, 3945_ATA|GCG, 3949_C|T,
3959_C|T, 3961_C|G, 3967_T|G, 3982_C|G, 3985_T|A, 4000_A|G, 4006_CG|AA, 4009_A|G, 4013_T|C, 4018_T|C, 4021_TG|CA, 4030_T|C, 4036_A|C, 4045_T|C, 4054, 4055_T|C, 4059_.|G, 4063_C|T, 4081_T|C,
4087_T|C, 4093_G|A, 4096_C|T, 4105_C|A, 4108_A|T, 4120_C|T, 4129_A|G, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4174_G|A, 4198_G|A, 4204_C|T, 4210_A|G, 4219_A|T, 4229_C|T, 4234_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4267_T|G, 4270_T|C, 4273_GA|AG, 4289_C|A, 4292_C|T, 4306_T|C, 4320_GG|AA, 4327_T|C, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4345_GC|AT, 4348_T|A, 4351_T|A,
4360_A|C, 4375_G|C, 4381_C|T, 4384_C|T, 4387_G|A, 4393_C|T, 4411_A|T, 4429_G|A, 4435_GC|AT, 4438_G|A, 4441_T|C, 4447_A|G, 4453_A|G, 4456_G|T, 4465_C|T, 4469_G|A, 4474_G|C, 4483_G|A, 4489_C|T,
4495_T|C, 4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CA, 4531_C|T, 4534_T|G, 4540_G|T, 4547_T|C, 4549_T|C, 4555_.|A, 4557_G|A, 4562, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G,
4600_T|A, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G, 4628_C|T, 4639_G|A, 4645_T|C, 4651_A|T, 4660_A|G, 4663_C|T, 4666_CT|TC, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4711_G|C,
4720_A|G, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4769_T|C, 4771_GA|AG, 4778_T|A, 4780_T|C, 4786_T|C, 4789_A|T, 4792_A|C, 4798_A|G, 4813_T|C, 4829_T|C, 4852_G|A,
4855_A|G, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4891_C|T, 4897_C|T, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|C, 4948_C|T, 4954_T|G,
4957_C|G, 4960_T|C, 4969_T|C, 4975_T|C, 4978_C|T, 4981_T|C, 4984_A|C, 4987_A|C, 4993_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5014_G|A, 5020_T|A, 5024_C|T, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T,
5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A, 5140_A|G, 5152_TG|CA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|G,
5176_T|C, 5179_G|A, 5185_A|T, 5190_.|C, 5195_C|T, 5200, 5206_CT|TC, 5212_C|T, 5215_G|A, 5230_CT|GC, 5239_T|G, 5245_G|T, 5251_C|T, 5257_C|T, 5260_G|A, 5269_T|C, 5272_T|C, 5287_T|C, 5299_G|A,
5302_C|T, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G, 5335_C|T, 5344_G|A, 5346_GA|AG, 5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5398_A|G, 5401_A|G, 5407_G|A, 5410_T|G, 5413_T|A, 5416_C|T,
5428_C|T, 5431_T|C, 5440_A|G, 5443_C|T, 5452_G|A, 5458_A|G, 5461_T|C, 5470_C|A, 5473_T|C, 5479_T|C, 5488_G|A, 5491_C|T, 5500_G|A, 5503_A|G, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5569_A|G,
5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5602_A|T, 5605_C|T, 5623_A|G, 5626_G|T, 5639_C|T, 5641_A|G, 5662_A|C, 5683_A|G, 5689_A|G, 5695_C|T, 5701_T|A, 5707_TT|CC, 5713_T|C, 5716_G|A, 5722_A|G,
5737_C|G, 5743_C|T, 5749_A|G, 5758_G|A, 5764_A|G, 5773_G|T, 5776_A|T, 5779_G|A, 5797_T|C, 5800_A|C, 5836_T|C, 5839_C|T, 5846_C|A, 5857_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G,
5929_C|T, 5932_C|A, 5935_A|T, 5938_C|T, 5941_T|C, 5947_T|C, 5953_G|A, 5956_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C,
6013_T|A, 6023_A|G, 6025_T|C, 6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6067_G|A, 6100_C|T, 6103_A|G, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6142_T|A, 6145_T|C, 6154_A|G,
6157_G|A, 6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6229_A|G, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|G, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|A,
6310_C|T, 6316_A|G, 6322_G|A, 6334_T|C, 6346_A|G, 6351_A|G, 6361_C|A, 6379_A|G, 6385_G|T, 6388_A|G, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G,
6433_T|C, 6442_A|G, 6445_T|G, 6448_T|G, 6451_A|G, 6457_A|G, 6463_G|A, 6478_T|G, 6481_T|C, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_CC|GA, 6535_C|T, 6547_C|T,
6550_T|C, 6569_C|T, 6571_A|G, 6595_A|G, 6611_A|G, 6613_A|G, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|A, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6730_A|G,
6733_C|T, 6757_TG|CA, 6766_C|A, 6772_C|T, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6829_C|T, 6835_A|G, 6841_A|T, 6844_C|T,
6850_T|C, 6859_CC|TT, 6866_C|T, 6874_A|T, 6876_C|T, 6883_A|T, 6889_C|T, 6892_G|A, 6895_A|G, 6902_C|T, 6904_G|A, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T, 6934_G|A, 6940_CT|TG,
6943_A|G, 6952_T|C, 6955_TG|CA, 6959_T|G, 6969_G|A, 6986_C|T, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|A, 7036_C|T, 7039_T|C, 7054_C|T, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T,
7085_C|T, 7096_A|T, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|A, 7138_A|C, 7141_A|G, 7156_T|C, 7162_G|T, 7171_G|C, 7177_GG|AA, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T,
7247_T|A, 7249_T|C, 7255_T|C, 7261_T|C, 7270_A|G, 7279_G|A, 7282_A|C, 7286_C|T, 7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7363_A|G,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C, 7426_CC|TT, 7429_A|G, 7432_T|C, 7450_A|G, 7453_G|C, 7456_C|T, 7463_T|C, 7465_G|A,
7468_T|C, 7480_CC|GT, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7528_T|C, 7531_T|G, 7540_A|G, 7543_C|T, 7552_C|G, 7567_C|T, 7571_A|C, 7573_G|A, 7580_C|T, 7597_A|T,
7612_A|C, 7630_A|G, 7634_C|A, 7642_C|A, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G, 7684_G|A, 7687_T|C, 7691_T|C, 7693_G|A, 7701_G|A, 7712_T|C, 7714_G|T, 7717_T|C, 7726_C|A, 7729_C|T, 7732_T|C,
7744_T|C, 7750_T|G, 7753_G|A, 7765_TT|CC, 7771_C|T, 7786_C|T, 7789_C|T, 7798_G|T, 7804_C|A, 7807_G|A, 7819_GT|AC, 7822_A|G, 7825_G|A, 7837_G|A, 7855_G|A, 7861_T|C, 7869_T|C, 7873_CC|TT,
7876_G|A, 7879_G|A, 7882_T|C, 7885_C|A, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A,
7990_T|C, 8011_C|T, 8014_C|T, 8020_C|T, 8023_A|G, 8044_A|G, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C, 8134_T|C,
8137_T|C, 8140_A|T, 8143_A|G, 8150_.|T, 8155, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T, 8186_T|C, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8233_A|G, 8245_C|T,
8248_A|G, 8251_A|G, 8254_G|C, 8266_T|C, 8269_C|T, 8275_G|A, 8278_T|C, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8320_TG|CA, 8329_T|C, 8338_C|T, 8341_A|G, 8354_C|T, 8362_G|A, 8365_A|G,
8371_G|A, 8374_T|C, 8380_T|A, 8383_A|C, 8392_C|T, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A, 8460_AA|GG, 8463_AG|CA, 8470_A|C, 8476_A|G, 8485_G|A,
8488_G|A, 8500_G|A, 8505_TGA|CAG, 8510_T|A, 8518_TT|CC, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8567_G|A, 8574_A|G, 8581_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T,
8608_T|A, 8611_T|G, 8617_A|G, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8683_T|C, 8692_G|A, 8704_T|C, 8707_A|G, 8725_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A,
8758_C|T, 8764_A|G, 8773_C|T, 8782_G|A, 8785_C|T, 8792_C|T, 8797_C|T, 8800_A|G, 8808_AC|GT, 8815_A|G, 8824_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|T, 8854_T|C, 8866_T|C, 8869_A|G,
8874_A|T, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8962_G|A, 8968_A|G, 8971_A|G, 8974_C|T, 8980_T|C, 9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A,
9052_C|T, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9091_T|A, 9100_G|A, 9106_G|T, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|A, 9136_C|T, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9175_A|G, 9179_T|C, 9181_C|T, 9187_A|C, 9190_T|C, 9201_A|G, 9212_A|C, 9214_G|A, 9217_T|A, 9229_C|T, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_CC|TT, 9280_T|G,
9313_C|T, 9322_C|T, 9325_A|G, 9328_A|G, 9336_AA|TG, 9343_G|A, 9349_A|G, 9361_G|A, 9367_A|G, 9379_GT|CC, 9382_G|A, 9391_C|T, 9397_A|T, 9406_C|A, 9416_G|A, 9427_A|G, 9430_A|G, 9439_A|G,
9445_C|T, 9467_C|T, 9478_C|A, 9484_CT|TC, 9490_A|G, 9493_C|T, 9505_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG, 9562_A|G, 9566_C|T,
9571_C|A, 9574_G|A, 9577_G|C, 9590_A|G, 9598_C|T, 9601_A|C, 9607_C|T, 9610_AC|GT, 9614_A|C, 9625_G|A, 9637_C|T, 9640_C|T, 9646_G|C, 9652_G|C, 9658_C|T, 9670_C|T, 9674_C|T, 9679_C|T, 9685_C|T,
9709_TA|GC, 9712_A|C, 9745_G|A, 9754_T|C, 9769_C|G, 9790_T|C, 9793_A|G, 9796_A|G, 9799_G|A, 9817_G|A, 9832_C|T, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_C|A, 9853_T|C, 9856_G|A, 9859_A|G,
9865_G|A, 9868_G|T, 9880_C|T, 9898_A|G, 9904_T|A, 9910_C|A, 9916_A|G, 9919_C|T, 9938_C|T, 9946_T|C, 9955_AA|GC, 9961_C|T, 9968_C|T, 9970_A|G, 9977_T|C, 9985_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|G, 10027_A|C, 10036_GA|TG, 10048_A|G, 10066_G|A, 10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10154_G|A, 10159_T|C,
10162_T|C, 10174_A|G, 10177_A|G, 10180_C|T, 10186_G|T, 10189_C|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10234_C|T, 10237_C|T, 10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_GC|AT, 10274_C|A, 10276_G|A, 10294_C|T, 10297_A|G, 10309_C|T, 10312_G|A, 10315_T|C, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10355_A|G, 10358_A|G,
10362, 10365_10372, 10374_AA|TG, 10377_C|A, 10381_10382, 10385, 10391_10397, 10404_10413, 10418_10422, 10425_C|T, 10427_10429, 10434_A|T, 10436_10439, 10442_C|A, 10446_10458, 10460,
10464_10475, 10522, 10524_G|A, 10526_C|T, 10533_A|G, 10535_T|A, 10547_A|G, 10554_CAC|TGT, 10558_A|G, 10568_C|T, 10605_ACC|CTT, 10620_A|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C,
10659_AG|CA, 10675_A|G, 10681_CT|TC, 10742_T|C

Case 3 (A.1): MW158361.1


Target: 835 samples Number of changes: 1490
BC: A.1 + A.1.NmC2 BC BR: 1476-1477 BC BR coord: 10527 - 10528
Direction L1: >> Initial region span: 1-1445,1485-1490Gap history (edge excluded): 1445-1485
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.94e+15 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1445 185.198001 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1485 6.21945 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 178_T|C, 221_G|A, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C,
327_AA|GG, 346_A|G, 349_C|A, 352_G|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 400_AT|TC, 409_A|G, 421_T|A, 427_T|C, 430_T|A, 434_C|T, 442_G|T, 448_C|T, 451_A|G, 454_TT|CC, 467_T|C, 475_G|T,
488_T|C, 496_G|C, 499_A|G, 501_A|G, 514_CC|TT, 517_A|G, 521_G|A, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T,
613_A|T, 619_A|G, 628_T|C, 634_T|C, 637_C|T, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T,
754_T|C, 757_C|T, 760_G|A, 763_T|C, 766_G|A, 790_C|T, 796_A|G, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 883_G|A, 886, 890_G|T,
891_.|G, 892_C|T, 898_C|T, 901_CC|TT, 904_T|A, 910_A|G, 931_C|T, 937_T|C, 941_C|T, 943_A|G, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G,
1066_C|T, 1069_T|C, 1072_T|G, 1090_T|C, 1094_T|C, 1102_C|A, 1108_A|G, 1111_G|A, 1117_A|T, 1123_T|C, 1127_A|G, 1138_G|A, 1140_TG|CA, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C,
1181_A|G, 1183_T|C, 1189_C|T, 1204_T|C, 1207_A|T, 1210_G|A, 1216_C|T, 1219_A|G, 1222_T|C, 1237_G|A, 1240_C|T, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G,
1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1327_A|G, 1342_A|G, 1351_TT|CC, 1366_T|C, 1372_C|T, 1378_T|C, 1387_C|T, 1393_A|G, 1400_T|C, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1432_TA|CG,
1435_C|T, 1447_T|C, 1453_G|A, 1474_C|T, 1480_A|G, 1482_TC|CT, 1486_G|A, 1491_T|C, 1495_G|A, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A,
1543_TG|CA, 1546_T|C, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1606_G|A, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1663_T|C, 1669_C|G, 1675_T|C,
1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1699_C|T, 1701_G|A, 1705_AC|GT, 1708_G|A, 1712_C|T, 1723_G|A, 1732_C|T, 1738_A|G, 1747_T|C, 1753_C|T, 1756_A|G, 1760_A|C, 1765_T|C, 1771_G|A, 1782_A|G,
1785_A|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C, 1819_T|A, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1879_C|T, 1882_A|G, 1887_T|C, 1915_C|A, 1926_TT|CC,
1942_A|G, 1946_T|C, 1969_T|C, 1975_G|A, 1978_A|G, 1981_A|G, 1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2026_A|G, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T,
2053_T|G, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2086_T|C, 2089_A|G, 2098_C|T, 2104_C|A, 2112_G|C, 2116_A|G, 2119_T|C, 2122_A|T, 2125_T|C, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G,
2188_A|G, 2193_T|C, 2197_A|G, 2209_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|T, 2230_T|C, 2239_C|T, 2248_G|A, 2251_C|T, 2254_C|T, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2269_A|G, 2275_T|A,
2278_T|C, 2280_C|T, 2296_C|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_AC|GT, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G, 2408_T|C, 2413_A|T, 2419_G|C, 2437_T|C, 2446_T|G,
2455_T|C, 2464_C|T, 2467_C|A, 2479_C|T, 2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2515_A|C, 2518_T|C, 2521_A|G, 2527_T|G, 2533_C|T, 2548_C|T, 2551_A|G, 2566_T|C, 2569_T|A,
2575_G|A, 2581_A|C, 2593_A|G, 2599_T|C, 2602_T|C, 2605_A|G, 2620_CC|TT, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2686_TT|CC, 2695_A|G, 2698_C|T,
2704_G|T, 2710_T|C, 2716_T|G, 2719_C|A, 2722_G|C, 2725_G|A, 2728_T|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2755_T|A, 2758_T|C, 2761_A|T, 2776_G|T, 2779_T|C, 2782_TC|CT, 2788_G|A, 2794_T|C,
2803_T|C, 2824_C|T, 2827_C|T, 2833_G|A, 2836_G|A, 2839_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2926_T|C, 2947_A|T, 2950_C|A, 2962_C|T, 2983_A|G,
2998_T|C, 3007_T|G, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3169_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G, 3265_A|G, 3271_A|G,
3289_T|C, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CA|TG, 3328_T|C, 3331_A|G, 3334_G|T, 3349_A|G, 3358_G|C, 3361_T|C, 3370_AG|GA, 3373_T|C, 3394_C|A, 3397_C|A,
3400_C|T, 3412_T|A, 3421_C|T, 3423_A|G, 3427_T|G, 3436_G|C, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3480_G|A, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3514_AA|GG, 3517_A|C,
3523_T|A, 3529_T|C, 3535_TT|GC, 3565_G|A, 3569_C|T, 3571_A|G, 3573_G|A, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3610_AG|CA, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3715_A|G, 3718_C|T, 3727_T|C, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3757_A|G,
3760_A|T, 3763_G|A, 3772_C|A, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3820_G|A, 3826_A|G, 3832_A|T, 3847_T|A, 3856_T|C, 3860_G|A, 3868_C|A, 3871_CC|GT, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C,
3901_C|T, 3908_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3945_ATA|GCG, 3949_CA|TG, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3967_T|G, 3982_C|G, 3985_T|A, 3998_A|C, 4006_CG|AA, 4009_A|G, 4013_T|C,
4015_C|T, 4021_TG|CA, 4030_T|C, 4036_A|C, 4045_T|C, 4056_TC|CA, 4066_C|T, 4070_A|G, 4081_T|C, 4087_TC|CT, 4096_C|T, 4105_C|G, 4108_A|T, 4120_C|A, 4129_A|G, 4135_TT|CC, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_C|A, 4171_T|C, 4174_G|A, 4183_T|C, 4198_G|A, 4204_C|T, 4210_A|G, 4216_T|C, 4219_A|C, 4229_C|T, 4234_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|G, 4270_T|C, 4274_A|G,
4289_C|A, 4291_C|T, 4306_T|C, 4321_G|A, 4330_G|A, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4357_T|C, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4411_A|T, 4429_G|A,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4456_G|C, 4465_C|T, 4469_G|A, 4474_G|C, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|A, 4523_C|A, 4531_C|T, 4544_C|T, 4547_T|C,
4557_G|A, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G, 4600_T|G, 4603_T|C, 4605_AG|CC, 4609_CA|TG, 4612_C|T, 4618_A|G, 4628_C|T, 4639_G|A, 4648_C|T, 4651_A|T, 4663_C|T,
4666_CT|TC, 4678_C|T, 4681_G|A, 4684_A|G, 4711_G|C, 4720_A|G, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4750_T|C, 4756_G|A, 4769_T|C, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4786_T|C,
4792_A|C, 4798_A|G, 4813_T|C, 4819_C|T, 4829_T|C, 4834_A|C, 4852_G|A, 4855_A|G, 4861_C|T, 4865_T|C, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A,
4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|C, 4942_A|G, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4978_C|T, 4981_T|C, 4984_A|C, 4987_A|C, 4990_T|A, 4993_T|C, 4999_T|C, 5011_A|T, 5020_T|A,
5024_C|T, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5101_A|G, 5107_G|A, 5110_G|A, 5116_A|G, 5119_G|A, 5134_A|G, 5140_A|G,
5152_TG|CA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|G, 5176_T|C, 5179_G|A, 5182_G|A, 5185_A|T, 5190_.|C, 5195_C|T, 5200, 5206_CT|TC, 5212_C|T, 5215_G|A, 5230_CT|GC, 5239_T|A, 5245_GT|CC,
5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5272_T|C, 5275_A|G, 5287_T|C, 5290_T|C, 5299_G|A, 5302_C|T, 5305_G|A, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G, 5335_C|T, 5344_G|A, 5346_GA|AG,
5368_C|T, 5374_C|T, 5380_A|G, 5383_T|A, 5393_T|C, 5398_A|G, 5401_A|T, 5407_G|A, 5410_T|G, 5413_T|A, 5428_C|T, 5431_T|C, 5443_C|T, 5449_T|C, 5452_G|A, 5458_A|G, 5461_T|C, 5470_C|A, 5473_T|C,
5479_T|C, 5488_G|A, 5491_C|T, 5500_G|A, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T, 5602_A|T, 5605_C|T, 5623_A|G, 5626_G|T, 5641_A|G,
5647_C|T, 5662_A|C, 5668_C|T, 5680_C|T, 5683_A|G, 5689_A|G, 5692_T|C, 5701_T|A, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_C|G, 5740_G|A, 5749_A|G, 5758_G|A, 5760_G|A, 5764_A|G, 5767_C|T,
5773_G|A, 5776_A|C, 5779_G|A, 5797_T|C, 5800_A|C, 5815_A|C, 5836_T|C, 5839_C|T, 5846_C|A, 5857_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|C, 5938_C|T,
5941_T|C, 5947_T|C, 5953_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6013_T|A, 6016_A|G, 6023_A|G, 6025_T|C, 6034_C|T,
6037_C|T, 6047_T|C, 6052_G|A, 6058_A|G, 6067_G|A, 6079_G|A, 6100_C|T, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6142_T|A, 6145_T|C, 6148_A|G, 6160_G|A, 6169_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|A, 6223_G|A, 6229_A|G, 6235_C|T, 6244_TT|AC, 6259_T|C, 6262_T|G, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|A, 6292_T|C, 6310_C|T, 6316_A|G, 6322_G|A,
6334_T|C, 6346_A|G, 6351_A|G, 6361_C|G, 6373_T|C, 6379_A|G, 6385_G|T, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6427_T|C, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6445_T|A,
6448_T|A, 6451_A|G, 6457_A|G, 6478_T|A, 6487_G|A, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6529_CC|TT, 6532_CC|GA, 6535_C|T, 6547_C|T, 6569_C|T, 6571_A|G, 6595_A|G,
6611_A|G, 6613_A|T, 6622_AC|GT, 6625_A|G, 6634_G|T, 6667_C|A, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6733_C|T, 6736_C|T, 6745_T|C, 6757_TG|CA, 6766_C|A,
6772_C|T, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6820_C|T, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6850_T|C, 6859_CC|TT, 6866_C|T,
6874_A|T, 6876_C|T, 6883_A|G, 6889_C|T, 6892_G|A, 6895_A|G, 6898_C|T, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T, 6934_G|A, 6940_C|T, 6943_AAT|GGC, 6949_A|G, 6952_T|C,
6956_G|A, 6958_TT|CG, 6969_GT|AC, 6976_G|A, 6986_C|T, 6988_G|A, 6994_A|G, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G, 7039_T|C, 7054_C|T, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7084_TC|CT, 7096_A|T, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7149_A|G, 7156_T|C, 7171_G|C, 7174_G|A, 7177_GG|AA, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T,
7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7279_G|A, 7286_C|T, 7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7411_CC|TT, 7414_T|G, 7420_T|C, 7423_C|T, 7426_CC|TT, 7432_T|C, 7450_A|G, 7453_G|C, 7456_C|T, 7465_G|A, 7468_T|C,
7480_CC|AT, 7483_A|G, 7492_T|A, 7495_CT|TC, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7519_C|T, 7527, 7531_.|G, 7540_A|G, 7552_C|G, 7571_A|C, 7580_C|T, 7597_A|T, 7612_A|T, 7630_A|G, 7634_C|A,
7642_C|A, 7651_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7696_C|T, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7729_C|T, 7732_T|C, 7744_T|C, 7750_T|G, 7753_G|A, 7762_G|A, 7765_TT|CC,
7771_C|T, 7789_C|T, 7798_G|C, 7804_C|G, 7807_G|A, 7816_A|T, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7855_G|A, 7861_T|C, 7869_T|C, 7874_C|T, 7876_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T,
7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7975_C|T, 7990_T|C, 8011_C|T, 8014_C|T, 8017_G|A, 8023_A|G, 8029_T|C,
8044_A|G, 8053_A|G, 8059_C|T, 8065_T|C, 8074_C|T, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C, 8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_G|T, 8154_C|G, 8158_T|C,
8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T, 8188_A|G, 8191_T|C, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8227_G|A, 8245_C|T, 8248_A|G, 8251_A|G, 8254_G|C, 8260_G|A, 8266_T|C, 8269_C|T,
8275_G|A, 8278_T|C, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8302_G|A, 8320_TG|CA, 8329_T|C, 8338_C|T, 8341_A|G, 8344_A|G, 8354_C|T, 8356_G|A, 8362_G|A, 8374_T|C, 8380_T|A, 8383_A|C,
8386_A|G, 8392_C|T, 8410_C|T, 8413_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CAG,
8510_T|A, 8512_T|C, 8519_T|C, 8539_C|T, 8551_C|T, 8554_C|T, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8608_T|A, 8611_T|G, 8617_A|G, 8629_T|C, 8632_A|T, 8638_C|T,
8650_G|A, 8653_C|T, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8792_C|T, 8797_C|T, 8800_A|G, 8808_A|G, 8815_A|G,
8824_A|C, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|T, 8854_T|C, 8866_T|C, 8874_A|T, 8917_C|T, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8968_A|G, 8971_A|G, 8974_C|T,
9007_G|A, 9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9118_T|C, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9163_A|G, 9166_C|T, 9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9187_A|C, 9190_T|C, 9201_A|G, 9208_T|A, 9212_A|T, 9214_G|A, 9217_T|A, 9229_C|T, 9232_C|T,
9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9301_G|A, 9307_C|T, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G, 9335_CAA|TTG, 9340_A|T, 9361_G|A, 9367_A|G, 9379_G|C,
9382_G|A, 9391_C|T, 9397_A|T, 9406_C|A, 9418_C|T, 9424_T|C, 9427_A|G, 9439_A|G, 9454_A|G, 9467_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9505_A|G, 9514_A|G, 9527_A|G, 9529_A|G, 9532_T|C,
9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9571_C|A, 9573_GG|AA, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C, 9607_C|T, 9610_AC|GT, 9637_C|T, 9646_G|T,
9652_G|C, 9658_C|T, 9664_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9709_TA|GC, 9712_A|C, 9745_G|A, 9754_T|C, 9769_C|G, 9775_T|C, 9778_C|T, 9790_T|C, 9796_A|G, 9799_G|A, 9817_G|A, 9820_T|C, 9835_A|G,
9838_A|T, 9841_G|A, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T, 9892_C|T, 9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A, 9916_A|G, 9919_C|T, 9922_T|C, 9928_C|T, 9938_C|T, 9946_T|C,
9955_A|G, 9958_G|A, 9961_C|T, 9970_A|G, 9977_T|C, 9985_T|C, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10024_C|T, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G,
10103_AC|GT, 10117_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10174_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10234_C|T, 10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_TA|CG, 10261_A|G, 10264_GC|AT, 10273_AC|GA, 10276_G|T,
10279_G|A, 10291_C|T, 10294_C|T, 10297_A|G, 10309_C|T, 10312_G|A, 10315_T|C, 10331_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10363, 10365_10369, 10371_10372,
10374, 10375_A|G, 10377_C|A, 10381_10382, 10385, 10391_10397, 10402_10410, 10414, 10418_10422, 10425_C|T, 10427_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10464_10475,
10522, 10524_G|A, 10526_C|T, 10533_A|G, 10535_T|A, 10549_C|A, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_ACC|CTT, 10620_A|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA,
10681_C|T

Case 3 (A.1): ON022716.1


Target: 835 samples Number of changes: 1409
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1342-1343 BC BR coord: 9798 - 9799
Direction L1: >> Initial region span: 1-1214,1344-1409Gap history (edge excluded): 1214-1344
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.92e-183Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1214 126.586032 NaN NaN NaN * * *
A.1.NmC1 0 32 3.704410 -416.610208 3671.220417 3.585207e-227
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1344 3.811378 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T,
664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_TT|CC, 784_G|A, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A,
1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG,
1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C,
1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_TG|CA, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G,
1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C,
2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C,
2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG,
2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_C|T, 2353_A|C, 2356_T|C,
2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T,
2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2611_G|A, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A,
2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2773_T|A, 2776_G|T, 2782_TC|CT, 2788_G|A, 2791_T|C, 2794_T|C,
2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2854_C|T, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G,
2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T,
3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_AC|GT, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T,
3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_GG|AA,
3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C,
3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G,
3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G,
3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G,
3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4099_C|T,
4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT,
4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A,
4372_G|A, 4375_G|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C,
4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T,
4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G,
4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A,
4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T,
5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5297_C|T, 5299_G|A, 5302_C|T,
5305_G|C, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C,
5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5512_T|C, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G,
5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A,
5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A,
5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6055_C|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A,
6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A,
6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_TA|CG, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G,
6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|A, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G,
6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA,
6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C,
7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7177_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G,
7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7399_G|A, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T,
7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT,
7597_A|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A,
7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T,
7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C,
7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A,
8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A,
8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T,
8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T,
8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8545_C|T, 8551_C|T,
8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G,
8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8767_T|A, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G,
8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8908_T|C, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|T, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9298_C|T, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9733_G|A, 9745_G|A, 9749_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA,
10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): OR119828.1


Target: 835 samples Number of changes: 1448
BC: A.1.NmC2 + A.1 BC BR: 12-13 BC BR coord: 280 - 281
Direction L1: >> Initial region span: 1-10,1421-1448Gap history (edge excluded): 10-1421
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.70e-04
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 10 6.029594 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1421 0.974331 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 271_T|C, 280_CA|TG, 289_T|C, 295_A|G, 304_A|T, 307_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 446_T|C, 448_C|T, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 496_G|C, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 559_C|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 610_C|T, 613_A|C, 628_T|C, 631_C|T,
649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCCAGAAG, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 802_A|G, 811_T|C, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 916_C|T, 931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A,
1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1181_A|G, 1183_T|C,
1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|C, 1249_C|T, 1255_C|A, 1261_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1288_T|C, 1294_A|G, 1306_G|A, 1321_C|T,
1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1433_A|G, 1435_C|T, 1441_T|C, 1444_G|A, 1462_C|T, 1465_G|T,
1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1501_A|G, 1504_A|G, 1507_T|C, 1510_A|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A, 1570_A|G,
1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT,
1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1804_T|C, 1807_T|G, 1810_A|G, 1813_T|C,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|A, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1900_C|T, 1915_C|A, 1921_C|T, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1951_A|G, 1957_C|G, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C,
2050_T|C, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2119_T|C, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G,
2188_A|G, 2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G, 2335_G|A, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C,
2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T,
2599_T|C, 2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C,
2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2761_A|T, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A,
2845_A|G, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A,
3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3086_A|G, 3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3184_G|A, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G,
3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3370_AG|GA, 3373_T|C,
3376_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|GT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC,
3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T,
3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C, 3778_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3826_A|G, 3829_A|G, 3832_A|T, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A,
3871_C|T, 3883_TC|CT, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3958_CC|TT, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4054_T|C, 4056_TC|CA, 4061_G|A, 4066_C|T, 4081_T|C, 4105_C|G, 4115_C|T, 4117_G|A, 4120_CT|AC, 4129_A|G, 4132_T|C, 4142_C|T,
4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4192_G|A, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4304_G|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T,
4399_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|A,
4522_TC|CT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4561_A|G, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T,
4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C,
4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4772_A|G, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4865_T|C, 4870_C|A, 4873_G|A, 4878_TT|CC,
4882_A|C, 4885_A|G, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T,
4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5077_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G,
5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5299_G|A, 5305_G|C, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5335_C|T, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T,
5368_C|T, 5374_C|T, 5378_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5639_C|T, 5641_A|G, 5644_T|G, 5650_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5821_A|G, 5833_C|T, 5839_C|T, 5846_C|A, 5872_T|C, 5875_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5965_T|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G,
6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G,
6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6172_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6205_C|T, 6211_C|T, 6220_T|C, 6223_G|A, 6241_T|C, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6299_T|C, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6373_T|C, 6388_A|G, 6403_G|C, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6424_T|C, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6467_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6835_A|G, 6841_A|C, 6844_C|T, 6847_C|T, 6850_T|C, 6860_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6904_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7030_A|G, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|A, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7252_C|T, 7255_TT|CC, 7258_A|G, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|AA, 7324_C|T, 7327_T|G, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT,
7405_A|G, 7411_C|T, 7414_T|G, 7417_T|C, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527,
7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7646_A|G, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7717_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G,
7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7861_T|A, 7864_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7939_A|G, 7945_T|C, 7956_GA|AG, 7960_C|A,
7966_T|C, 7969_G|A, 7972_A|G, 7990_T|C, 7996_A|G, 8011_C|T, 8020_C|T, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A,
8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8173_C|T, 8176_T|C, 8185_G|A, 8188_A|G, 8209_T|G, 8212_C|T,
8215_G|A, 8218_A|G, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8272_C|T, 8275_G|A, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8324_A|G, 8326_A|G, 8329_T|C,
8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T,
8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_.|C, 8507, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8574_A|G,
8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8785_C|T, 8788_C|T, 8792_C|T, 8797_C|T, 8801_G|A, 8806_G|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8836_T|C,
8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GA|AC, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8995_C|T,
9009_9010, 9017_.|AA, 9022_G|A, 9037_G|A, 9043_A|G, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9087_A|T, 9100_G|A, 9103_C|T, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G,
9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9187_A|C, 9190_T|C, 9205_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9226_A|T, 9229_C|T, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G,
9295_G|A, 9298_C|T, 9313_C|T, 9317_C|T, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9355_A|T, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T,
9397_A|T, 9424_T|C, 9427_A|G, 9460_T|C, 9463_T|C, 9466_T|C, 9472_C|T, 9475_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_GG|AA, 9577_G|T, 9580_G|A, 9590_AC|GT, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9676_G|A, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9844_C|T,
9850_CA|AG, 9856_G|C, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10072_C|T, 10081_G|A, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10240_TT|CC, 10243_A|G, 10246_C|A, 10249_C|A, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10355_A|G, 10361_10369, 10371_10375, 10378_10387, 10391_10397,
10401_10412, 10417, 10420_10421, 10424_10427, 10430_10437, 10439_10441, 10447_10450, 10452_10454, 10457, 10458_C|T, 10460_C|T, 10463_T|A, 10467_10470, 10475_AGA|TTG, 10522, 10524_G|A,
10533_A|G, 10535_T|A, 10647_C|T, 10658_AG|CC, 10662_.|T, 10681_CT|TC, 10703_C|T, 10802_.|T, 10817, 10843_AT|TA, 10847_C|A, 10849_A|G

Case 3 (A.1): PQ186339.1


Target: 835 samples Number of changes: 1482
BC: A.1 + A.1 BC BR: 1443-1444 BC BR coord: 10372 - 10373
Direction L1: >> Initial region span: 1-1433,1447-1482Gap history (edge excluded): 1433-1447
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.29e-12
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1433 189.933617 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1447 3.326184 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_G|A, 320_T|C, 327_A|G, 346_A|G,
349_C|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 388_TT|CC, 400_A|T, 409_A|G, 421_T|A, 425_C|T, 430_T|A, 433_TC|CT, 442_G|T, 448_C|T, 454_T|C, 467_T|C, 475_G|T, 488_T|C, 496_G|C, 499_A|G,
501_A|G, 514_CC|TT, 517_A|G, 523_G|C, 535_C|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 628_T|C, 634_T|C, 649_G|A, 655_A|T, 664_T|A,
667_T|C, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 727_732, 734_736, 747_.|GTCTAGAAG, 757_C|T, 760_G|A, 763_T|C, 766_G|A, 790_C|T, 802_A|G, 823_T|C,
826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 892_C|T, 898_C|T, 901_CC|TT, 904_T|A, 910_A|G, 931_C|T, 940_CC|TT,
943_A|G, 946_G|A, 949_C|T, 961_T|C, 964_G|A, 967_C|T, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 997_C|T, 1036_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|T, 1072_T|G, 1090_T|C, 1094_T|C,
1102_C|A, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1183_T|C, 1189_C|T, 1195_C|T, 1204_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT,
1219_A|G, 1222_T|C, 1228_G|A, 1234_A|G, 1237_G|A, 1240_CA|TC, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G, 1282_T|C, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A,
1321_C|T, 1333_T|C, 1339_C|T, 1342_A|G, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1433_A|G, 1435_C|T, 1438_C|T, 1453_G|A,
1471_C|T, 1474_C|T, 1480_A|G, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1531_T|C, 1534_G|A, 1544_G|A, 1546_T|C, 1552_T|C, 1558_C|T,
1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1606_G|A, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A,
1705_AC|GT, 1711_C|T, 1723_G|A, 1732_CT|TC, 1738_A|G, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1782_A|G, 1785_A|G, 1790_C|T, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_T|C, 1818_CT|TA, 1822_C|T, 1855_G|A, 1858_A|G, 1861_C|T, 1867_A|G, 1870_A|G, 1876_T|C, 1879_C|T, 1887_T|C, 1900_C|T, 1909_C|T, 1915_C|A, 1926_TT|CC, 1939_G|A, 1946_T|C, 1969_T|C,
1978_A|G, 1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2053_T|G, 2059_A|G, 2063_C|T, 2080_A|C, 2083_T|C, 2086_T|C, 2089_A|G,
2092_C|T, 2098_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2119_T|C, 2122_A|T, 2128_C|G, 2146_A|G, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_T|C, 2197_A|G, 2201_C|T, 2209_C|T, 2215_A|G,
2218_CA|TG, 2221_C|T, 2224_C|T, 2230_T|C, 2233_C|T, 2239_C|T, 2248_G|A, 2251_C|T, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2269_A|G, 2275_T|A, 2278_T|C, 2280_C|T, 2305_G|A, 2308_A|G, 2314_C|T,
2318_T|C, 2322_AC|GT, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G, 2395_C|T, 2408_T|C, 2413_A|T, 2419_G|T, 2432_T|C, 2437_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2467_C|A, 2488_G|A, 2494_G|A,
2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2515_A|C, 2521_A|G, 2524_C|T, 2527_T|G, 2533_C|T, 2548_C|T, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|C, 2593_A|G, 2599_T|C, 2602_T|C, 2605_A|G,
2620_CC|TT, 2626_T|C, 2632_T|C, 2635_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2686_TT|CC, 2695_A|G, 2698_C|T, 2701_G|A, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G,
2722_G|C, 2725_G|A, 2728_T|C, 2731_A|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|T, 2776_G|T, 2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2821_G|A, 2827_C|T,
2830_A|G, 2833_G|A, 2836_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 3007_T|G, 3013_G|A,
3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3145_G|A, 3169_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3250_A|G, 3268_A|G, 3271_A|G,
3289_T|C, 3298_G|A, 3301_T|C, 3304_C|T, 3307_GA|AG, 3310_CA|TG, 3316_T|C, 3319_CAA|TGG, 3328_T|C, 3334_G|T, 3337_A|G, 3349_A|G, 3358_G|C, 3364_C|T, 3370_AG|GA, 3373_T|C, 3382_A|G, 3394_C|A,
3397_C|A, 3400_C|T, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3511_A|G,
3514_AA|GG, 3517_A|C, 3523_T|A, 3535_TT|GC, 3566_G|T, 3569_C|T, 3571_A|G, 3573_G|A, 3577_A|G, 3589_A|C, 3598_G|A, 3610_AG|CA, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3658_T|C, 3664_G|A, 3667_A|G, 3670_CAC|AGT, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3727_T|C,
3733_G|C, 3739_T|A, 3745_C|T, 3751_A|G, 3757_A|G, 3760_A|T, 3763_G|A, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3820_G|A, 3826_A|G, 3832_A|C, 3835_C|T, 3847_T|A, 3856_T|C, 3860_G|A, 3868_C|A,
3871_C|G, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3910_G|A, 3931_T|C, 3934_G|A, 3940_A|G, 3946_TA|CG, 3949_C|A, 3953_T|C, 3959_C|T, 3961_C|G, 3967_T|G, 3982_C|G, 3985_T|A,
4006_CG|AA, 4009_A|G, 4013_T|C, 4021_TG|CA, 4030_T|C, 4034_A|G, 4036_A|C, 4045_T|C, 4054_T|C, 4056_TC|CA, 4060_G|A, 4066_C|T, 4075_G|A, 4081_T|C, 4087_T|C, 4105_C|G, 4108_A|T, 4120_C|A,
4129_A|G, 4142_C|T, 4150_A|C, 4154_C|A, 4165_C|A, 4171_T|C, 4174_G|A, 4177_A|G, 4183_T|C, 4198_G|A, 4204_C|T, 4210_A|G, 4219_A|C, 4229_C|T, 4234_A|G, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|G,
4270_T|C, 4274_A|G, 4289_C|A, 4291_C|T, 4304_G|A, 4306_T|C, 4321_G|A, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T,
4399_C|T, 4411_A|T, 4423_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4444_T|C, 4453_A|G, 4456_G|T, 4465_C|T, 4469_G|A, 4474_G|C, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4519_T|A,
4522_TC|CA, 4531_C|T, 4540_G|T, 4544_C|T, 4547_T|C, 4549_T|C, 4557_G|A, 4561_A|G, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4597_CA|TG, 4600_T|A, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G,
4627_TC|CT, 4630_G|A, 4639_G|A, 4651_A|T, 4660_A|G, 4663_C|T, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4711_G|C, 4720_A|G, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4753_C|T,
4756_G|A, 4769_T|C, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4792_A|C, 4813_T|C, 4819_C|T, 4829_T|C, 4834_A|G, 4840_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|T, 4873_G|A, 4876_T|C,
4878_TT|CC, 4882_A|C, 4891_C|T, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|C, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4981_T|C, 4984_A|C, 4987_A|C,
4993_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5014_G|A, 5020_T|A, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5103_A|G,
5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A, 5140_A|G, 5152_TG|AA, 5155_C|T, 5161_T|C, 5164_T|C, 5170_T|C, 5173_A|G, 5176_T|C, 5179_G|A, 5182_G|A, 5185_A|T, 5188_A|G, 5190_.|C, 5195_C|T, 5200,
5206_CT|TC, 5212_C|T, 5215_G|A, 5218_C|T, 5230_CT|GC, 5239_T|G, 5245_GT|TC, 5251_C|T, 5257_C|T, 5269_T|C, 5272_T|C, 5275_A|G, 5287_T|C, 5293_C|T, 5299_G|A, 5305_G|A, 5308_A|G, 5323_T|C,
5326_T|C, 5332_T|G, 5335_C|T, 5344_G|A, 5346_GA|AG, 5368_C|T, 5371_T|C, 5374_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5393_T|C, 5398_A|G, 5407_G|A, 5410_T|G, 5413_T|G, 5416_C|T, 5422_A|G, 5440_A|G,
5443_C|T, 5458_A|G, 5461_T|C, 5470_C|A, 5473_T|C, 5479_T|C, 5488_G|A, 5491_C|T, 5500_G|A, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T,
5602_A|T, 5605_C|T, 5620_C|T, 5623_A|G, 5626_G|T, 5638_CC|TT, 5641_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5689_A|G, 5692_T|C, 5701_T|A, 5708_T|C, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_C|G,
5740_G|A, 5749_A|G, 5758_G|A, 5760_G|A, 5764_A|G, 5773_G|A, 5776_A|T, 5779_G|A, 5797_T|C, 5800_A|C, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5857_T|C, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G,
5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5938_C|T, 5941_T|C, 5947_T|C, 5953_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T,
6004_T|C, 6013_T|A, 6023_A|G, 6025_T|C, 6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6070_C|T, 6088_T|C, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6142_T|A, 6154_AC|GT,
6157_G|A, 6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C, 6187_AC|GT, 6199_T|C, 6211_C|T, 6214_T|C, 6220_T|C, 6223_G|A, 6229_A|G, 6232_G|T, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6280_C|T,
6283_T|A, 6292_T|C, 6299_T|C, 6310_C|T, 6316_A|G, 6322_G|A, 6334_T|C, 6351_A|G, 6361_C|G, 6367_G|A, 6373_T|C, 6379_A|G, 6385_G|T, 6400_T|C, 6403_G|C, 6406_GT|TG, 6409_T|C, 6415_T|C, 6427_T|C,
6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6445_T|G, 6448_T|A, 6451_A|G, 6457_A|G, 6478_T|A, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6529_CC|TT, 6532_CC|GA, 6547_C|T,
6550_T|C, 6569_C|T, 6571_A|G, 6595_A|G, 6611_A|G, 6613_A|T, 6622_AC|GT, 6625_A|G, 6634_G|T, 6664_A|G, 6667_C|A, 6670_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6709_T|C, 6715_T|C,
6724_C|T, 6730_A|G, 6733_C|T, 6745_T|C, 6757_TG|CA, 6766_C|G, 6769_A|C, 6772_C|T, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6805_A|G, 6811_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6835_A|G,
6841_A|T, 6844_C|T, 6850_T|C, 6859_C|T, 6866_C|T, 6874_A|C, 6876_C|T, 6880_G|A, 6883_A|G, 6889_C|T, 6895_A|G, 6898_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T, 6934_G|A, 6940_C|T,
6943_A|G, 6952_T|C, 6955_TG|CA, 6958_TT|CG, 6969_GT|AC, 6976_G|A, 6986_C|T, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G, 7030_A|G, 7039_T|C, 7046_T|C, 7054_C|T, 7063_A|G,
7066_C|T, 7069_A|G, 7079_C|T, 7081_G|A, 7084_T|C, 7114_CC|TT, 7117_T|G, 7120_T|A, 7129_C|T, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|C, 7174_G|A, 7177_GG|AA, 7180_C|T, 7211_C|T,
7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7273_G|A, 7279_G|A, 7286_C|T, 7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T,
7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7450_A|G, 7453, 7459_.|C, 7465_G|A, 7468_T|C, 7480_CC|AT, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7519_C|T, 7528_T|C, 7531_T|G, 7552_C|G, 7561_A|G, 7571_A|C,
7580_C|T, 7582_C|T, 7597_A|T, 7612_A|C, 7630_A|G, 7634_C|A, 7642_C|A, 7645_G|A, 7651_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7691_T|C, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7744_T|C,
7750_T|A, 7753_G|A, 7762_G|A, 7765_T|C, 7771_C|T, 7789_C|T, 7798_G|T, 7804_C|G, 7807_G|A, 7813_C|T, 7816_A|T, 7819_GT|AC, 7822_A|G, 7825_G|A, 7837_G|A, 7840_T|C, 7843_C|T, 7855_G|A, 7861_T|C,
7869_T|C, 7876_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_T|C,
8011_C|T, 8014_C|T, 8023_A|G, 8025_C|T, 8041_A|G, 8044_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8077_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8095_A|G, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C,
8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_GGC|TAG, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|A, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8248_A|G, 8251_A|G,
8254_G|C, 8260_G|A, 8266_T|C, 8269_C|T, 8275_G|A, 8278_T|C, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8302_G|A, 8305_T|A, 8314_C|T, 8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G,
8350_C|T, 8354_C|T, 8362_G|A, 8374_T|C, 8380_T|A, 8383_A|C, 8392_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|C,
8476_A|G, 8485_G|A, 8488_G|A, 8505_TGA|CAG, 8510_T|A, 8512_T|C, 8518_TT|CC, 8551_C|T, 8557_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G,
8614_T|C, 8617_A|G, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8707_A|G, 8719_C|T, 8722_C|A, 8743_G|T, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G,
8770_C|T, 8773_C|T, 8782_G|A, 8785_C|T, 8797_C|T, 8800_A|G, 8808_A|G, 8815_A|G, 8824_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|C, 8854_T|C, 8866_T|C, 8874_A|T, 8923_C|T, 8926_A|G,
8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8962_G|A, 8968_A|G, 8971_A|G, 8974_C|T, 9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C,
9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|A, 9136_C|T, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9187_A|C, 9190_T|C,
9203_C|T, 9208_T|C, 9212_A|C, 9214_G|A, 9217_T|A, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G,
9335_CAA|TTG, 9343_G|A, 9361_G|A, 9367_A|G, 9379_G|C, 9382_G|A, 9391_C|A, 9397_A|T, 9400_G|A, 9403_A|G, 9406_C|A, 9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G, 9445_C|T, 9454_A|G, 9467_C|T,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9505_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG, 9562_A|G, 9565_T|C, 9570_CC|TA, 9573_GG|AA, 9577_G|T,
9590_A|G, 9598_C|T, 9601_A|C, 9607_C|T, 9610_AC|GT, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|C, 9658_C|T, 9670_C|T, 9676_G|A, 9679_C|T, 9685_C|T, 9709_TA|GC, 9712_A|C, 9745_G|A, 9754_T|C,
9769_C|G, 9775_T|C, 9784_C|T, 9790_T|C, 9796_A|G, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T, 9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A,
9916_A|G, 9919_C|T, 9938_C|T, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10024_C|T, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A,
10066_G|A, 10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10154_G|A, 10159_T|C, 10162_T|C, 10174_A|G, 10186_G|T, 10213_T|C, 10216_G|A, 10222_C|T,
10228_C|A, 10231_C|T, 10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10294_C|T, 10297_A|G, 10312_G|A, 10315_T|C, 10336_A|G,
10338_TG|CC, 10342_T|C, 10348_T|C, 10355_A|G, 10358_A|G, 10363_C|T, 10365_AA|TG, 10369_10377, 10381_10382, 10385, 10391_10397, 10403_10405, 10407, 10409_10411, 10412_C|G, 10416_10417,
10418_C|T, 10421_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10462, 10465_10475, 10522, 10524_G|A, 10526_C|T, 10528_G|A, 10533_A|G, 10535_T|G, 10554_CAC|TGT, 10558_A|G,
10562_T|C, 10605_A|C, 10607_C|T, 10620_A|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10681_C|T, 10685_C|T, 10740_A|G, 10817_T|C, 10847_C|A

Case 3 (A.1): PQ186344.1


Target: 835 samples Number of changes: 1445
BC: A.1.NmC2 + A.1 + A.1.NmC2BC BR: 163-164, 1441-1442 BC BR coord: 1407 - 1408, 10532 - 10533
Direction L1: >> Initial region span: 1-119,1432-1441,1442-1445Gap history (edge excluded): 119-1442 -> 119-1432
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.04e-123
Rec. model vs L1: 8.46e-302 Rec. model vs L2: 4.42e-06
Flags: Model_2BP_Best

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 119 7.738257 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1432 3.072210 NaN NaN NaN * * *
A.1.NmC1 0 1442 0.000000 -1728.884026 6423.768051 0.000000e+00
A.1.NmC2 0 1441 -0.122999 -349.547923 3665.095847 3.043373e-123
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1442 7.352352 None None None * * *



Target sequence

, 80_A|G, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 280_CA|TG, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|T, 327_A|G,
346_A|G, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 424_C|T, 427_T|A, 434_C|T, 448_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 706_T|C, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCCAGAAG, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 811_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1066_C|T, 1072_T|G,
1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1249_C|T, 1255_C|A, 1261_T|C, 1279_C|A, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C,
1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|T, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1504_A|G, 1507_T|C, 1516_A|G, 1525_G|T, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1593_G|A, 1606_G|A, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|C, 1747_T|C, 1753_C|T,
1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C,
1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1951_A|G, 1957_C|A, 1966_G|A, 1969_T|C, 1975_G|A, 1978_A|G,
1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2089_A|G,
2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_GA|CT, 2116_A|G, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|T, 2164_A|G, 2188_A|G, 2193_TG|CA, 2197_A|G, 2201_C|T, 2215_A|G, 2218_CA|TG,
2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_A|G,
2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A,
2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2518_T|C, 2524_C|T, 2527_T|A, 2541_A|G, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|T, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2821_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G,
2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2905_T|C, 2908_T|C, 2920_G|A, 2932_G|A, 2938_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C,
3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3098_T|C, 3104_GC|AT, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3355_C|T, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3649_TC|CA, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3688_G|A, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C,
3763_G|A, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3821_A|G, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3895_T|A, 3898_T|C,
3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_GG|CA, 4042_C|T, 4045_T|C,
4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4099_C|T, 4105_C|G, 4117_G|A, 4120_CT|AC, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4285_A|G, 4289_C|A, 4306_T|C,
4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4345_G|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A,
4441_T|C, 4450_G|A, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|C, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4547_T|C, 4549_T|C,
4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A,
4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A,
4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4798_A|G, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G,
4888_G|A, 4891_C|T, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4924_C|T, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T,
4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5053_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G,
5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5125_G|A, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|C, 5207_T|C, 5212_C|T, 5215_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5257_C|T, 5260_G|A, 5284_G|A, 5287_T|C, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5314_C|T, 5323_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T,
5374_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5639_C|T, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G,
5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C,
5989_A|G, 6004_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6124_T|A, 6127_A|G, 6142_T|A,
6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6241_T|C, 6244_T|A, 6253_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G,
6283_T|A, 6286_G|A, 6292_T|C, 6310_C|T, 6316_A|G, 6319_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6367_G|A, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A,
6421_G|A, 6430_A|G, 6433_T|C, 6439_G|A, 6451_AG|GA, 6457_A|G, 6460_T|C, 6472_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T,
6532_C|G, 6544_A|G, 6547_C|T, 6550_T|C, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6748_C|T, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6818_T|A, 6823_C|T,
6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6934_G|A, 6940_C|T, 6943_A|G,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T,
7247_T|A, 7255_TT|CC, 7258_A|G, 7267_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_T|A, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7456_C|T, 7463_T|C, 7480_C|G, 7483_A|G, 7486_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7527, 7531_.|G, 7552_C|G,
7571_A|C, 7579_TC|CT, 7585_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7690_GT|AC, 7699_G|A, 7701_GA|AG,
7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G,
7837_G|A, 7849_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7920_AG|GA, 7924_A|G, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C,
7956_GA|AG, 7960_C|A, 7963_C|T, 7966_T|C, 7969_G|A, 7990_T|C, 7996_A|G, 8011_C|T, 8020_C|T, 8023_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC,
8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A,
8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8326_A|G, 8329_T|C,
8338_C|T, 8347_C|T, 8354_C|T, 8356_G|A, 8362_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_CC|TT, 8395_G|T, 8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A,
8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C,
8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A,
8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8725_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T,
8851_A|C, 8860_A|G, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8929_G|A, 8939_C|T, 8941_G|A, 8953_AA|GC, 8956_GAA|ACG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8986_T|C,
9009_9010, 9017_.|AA, 9022_G|A, 9031_G|A, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T,
9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9205_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9263_A|G, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|A,
9295_G|A, 9298_C|T, 9313_C|T, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T,
9424_T|C, 9427_A|G, 9430_A|G, 9448_G|A, 9454_A|G, 9460_T|C, 9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9497_T|C, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_GG|AA, 9577_G|T, 9590_A|G, 9595_G|A, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9625_G|A, 9637_C|T, 9643_T|C, 9646_G|T, 9658_C|T,
9670_C|T, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9763_T|C, 9766_G|A, 9769_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9865_G|A, 9880_C|T, 9898_A|G, 9904_T|A, 9907_C|T, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10072_C|T, 10096_A|G, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10303_C|T, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T,
10355_A|G, 10362, 10365_10366, 10368_10372, 10373_T|C, 10376_10379, 10382, 10385, 10391_10397, 10403_C|T, 10408_10416, 10418_C|T, 10421_A|T, 10423_10424, 10426_10430, 10435_10447,
10450_10460, 10465_10476, 10522, 10524_G|A, 10533_A|G, 10535_T|A, 10844_T|C, 10847_C|A

Case 3 (A.1): PQ186349.1


Target: 835 samples Number of changes: 1487
BC: A.1 + A.1 BC BR: 1468-1469 BC BR coord: 10521 - 10522
Direction L1: >> Initial region span: 1-1468,1485-1487Gap history (edge excluded): 1468-1485
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.92e-08
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1468 207.372904 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1485 1.043567 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 178_T|C, 226_C|T, 247_T|C, 262_C|T, 265_T|C, 280_CA|TG, 284_T|C, 294_AA|GG, 304_A|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C, 327_A|G, 332_C|T,
346_A|G, 349_C|A, 352_G|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 388_TT|CC, 400_A|T, 409_A|G, 421_T|A, 430_T|A, 433_TC|CT, 442_G|T, 448_C|T, 451_A|G, 454_T|C, 467_T|C, 475_G|T, 488_T|C,
496_G|C, 499_A|G, 501_A|G, 514_CC|TT, 517_A|G, 523_G|C, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 628_T|C, 634_T|C,
637_C|T, 649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 723_CA|TG, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 757_C|T, 760_G|A, 763_T|C, 766_G|A,
778_T|C, 790_C|T, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 871_T|C, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 892_C|T, 898_C|T, 902_C|T,
904_T|A, 910_A|G, 931_C|T, 940_CC|TT, 943_A|G, 949_C|T, 961_T|C, 964_G|A, 967_C|T, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 1030_T|C, 1036_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|T,
1072_T|G, 1090_T|C, 1102_C|A, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1183_T|C, 1189_C|T, 1204_T|C, 1207_A|T, 1210_G|A,
1214_C|T, 1216_CC|TT, 1219_A|G, 1222_T|C, 1228_G|A, 1234_A|G, 1237_G|A, 1240_CA|TC, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G, 1282_T|C, 1294_A|G,
1300_G|A, 1306_G|A, 1309_C|T, 1321_C|T, 1333_T|C, 1339_C|T, 1342_A|G, 1345_C|T, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1408_A|T, 1411_G|A, 1414_C|T, 1423_A|G,
1426_T|C, 1433_A|G, 1435_C|T, 1438_C|T, 1453_G|A, 1471_C|T, 1474_C|T, 1480_A|G, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1511_C|T, 1516_A|G, 1522_G|A, 1525_G|A,
1528_A|G, 1531_T|C, 1534_G|A, 1544_G|A, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C,
1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1723_G|A, 1732_CT|TC, 1738_A|G, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1782_A|G, 1785_A|G, 1792_T|G, 1798_A|G,
1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C, 1819_T|A, 1822_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1879_C|T, 1887_T|C, 1900_C|T, 1915_C|A, 1926_TT|CC, 1946_T|C, 1951_A|G,
1963_C|T, 1969_T|C, 1978_A|G, 1990_T|C, 1993_T|C, 1996_A|G, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2041_C|T, 2044_A|C, 2047_C|T, 2053_T|G,
2080_A|C, 2083_T|C, 2086_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2112_GA|CG, 2116_A|G, 2119_T|C, 2122_A|T, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G, 2188_A|G, 2193_TG|CA,
2197_A|G, 2201_C|T, 2209_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|A, 2230_T|C, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2266_G|A, 2275_T|A, 2278_T|C, 2280_C|T, 2290_C|T, 2305_GC|AT,
2308_A|G, 2314_C|T, 2322_AC|GT, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G, 2383_C|T, 2395_C|T, 2408_T|C, 2413_A|T, 2419_G|C, 2432_T|C, 2437_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2467_C|A,
2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2515_A|C, 2518_T|C, 2521_A|G, 2524_C|T, 2527_T|A, 2533_C|T, 2548_C|T, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|C, 2593_A|G, 2599_T|C,
2602_T|C, 2605_A|G, 2620_CC|TT, 2626_T|C, 2632_T|C, 2635_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2687_T|C, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|A,
2722_G|C, 2725_G|A, 2728_T|C, 2731_A|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|T, 2776_G|T, 2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2824_C|T, 2827_C|T,
2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 3007_T|G, 3013_G|A, 3019_C|T, 3022_A|G,
3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3070_A|G, 3073_A|G, 3076_T|C, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3169_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G, 3271_A|G, 3277_G|A, 3289_T|C, 3298_G|A,
3301_T|C, 3308_A|G, 3310_CA|TG, 3316_TG|CA, 3319_CAA|TGG, 3334_G|T, 3337_A|G, 3349_A|G, 3358_G|C, 3361_T|C, 3364_C|T, 3370_AG|GA, 3373_T|C, 3382_A|G, 3394_C|A, 3397_C|A, 3400_C|T, 3412_T|A,
3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_GC|AT, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3511_A|G, 3514_AA|GG, 3517_A|C,
3523_T|A, 3535_TT|GC, 3566_G|T, 3569_C|T, 3571_A|G, 3573_G|A, 3576_A|G, 3589_A|C, 3598_G|A, 3601_G|A, 3610_AG|CA, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3649_T|C, 3652_C|A, 3655_T|G, 3658_TT|CC, 3662_C|T, 3667_A|G, 3670_CAC|TGT, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3727_T|C, 3733_G|C,
3739_T|C, 3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3760_A|G, 3763_G|A, 3778_T|C, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3820_G|A, 3824_C|T, 3826_A|G, 3832_A|T, 3841_G|A, 3847_T|A, 3851_T|C,
3856_T|C, 3860_G|A, 3868_C|A, 3871_C|G, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3931_T|C, 3940_A|G, 3944_AATA|GGCG, 3952_CT|TC, 3959_C|T, 3961_C|G, 3967_TC|GT, 3973_G|A,
3982_C|G, 3985_TA|AC, 4006_CG|AA, 4009_A|G, 4013_T|C, 4021_TG|CA, 4030_T|C, 4045_T|C, 4054_T|C, 4056_TC|CA, 4066_C|T, 4069_C|A, 4075_G|A, 4081_T|C, 4084_A|G, 4087_T|C, 4105_C|G, 4108_A|T,
4120_C|A, 4129_A|G, 4138_G|A, 4142_C|T, 4150_A|C, 4152_T|A, 4154_C|A, 4159_A|G, 4165_C|A, 4171_T|C, 4174_G|A, 4183_T|C, 4198_G|A, 4204_C|T, 4210_A|G, 4219_A|C, 4229_C|T, 4246_T|C, 4264_C|T,
4267_T|G, 4270_T|C, 4274_A|G, 4289_C|A, 4291_C|T, 4304_G|A, 4306_T|C, 4321_G|A, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4360_A|T, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T,
4399_C|T, 4411_A|T, 4423_A|G, 4429_G|A, 4436_C|T, 4438_G|A, 4441_T|C, 4453_A|G, 4456_G|C, 4465_C|T, 4469_G|A, 4474_G|C, 4483_G|A, 4489_C|T, 4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CA,
4531_C|T, 4540_G|T, 4544_C|T, 4547_T|C, 4549_T|C, 4557_G|A, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G, 4600_T|A, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G, 4627_TC|CT,
4630_G|A, 4639_G|A, 4651_A|C, 4660_A|G, 4663_C|T, 4666_CT|TC, 4669_G|A, 4678_C|T, 4684_A|G, 4711_G|C, 4720_A|G, 4732_C|G, 4738_A|G, 4741_A|T, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A,
4768_GT|AC, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4792_A|C, 4819_C|T, 4829_T|C, 4834_A|G, 4840_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C,
4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4930_G|T, 4939_G|C, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4978_C|T, 4981_T|C, 4984_A|C, 4987_A|C, 4993_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5014_G|A, 5020_T|A, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5103_A|G, 5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A,
5140_A|G, 5152_TG|AA, 5155_C|T, 5161_T|C, 5164_T|C, 5170_T|C, 5173_A|G, 5176_T|C, 5179_G|A, 5182_G|A, 5185_A|T, 5189_A|G, 5190_.|G, 5192_T|A, 5195_C|T, 5200, 5206_CT|TC, 5212_C|T, 5215_G|A,
5218_C|T, 5230_C|G, 5239_T|G, 5245_GT|TC, 5251_C|T, 5254_C|T, 5257_CA|TC, 5272_T|C, 5275_A|G, 5287_T|C, 5293_C|T, 5299_G|A, 5302_C|T, 5305_G|A, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G,
5335_C|T, 5344_G|A, 5346_GA|AG, 5368_C|T, 5371_T|C, 5380_A|G, 5383_T|A, 5389_G|A, 5393_T|C, 5398_A|G, 5407_G|A, 5410_T|G, 5413_T|G, 5416_C|T, 5422_A|G, 5428_C|T, 5431_T|C, 5440_A|G, 5443_C|T,
5452_G|A, 5458_A|G, 5461_T|C, 5470_C|A, 5473_T|C, 5479_T|C, 5488_G|A, 5500_G|A, 5530_A|T, 5539_G|C, 5542_T|A, 5545_G|A, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T, 5602_A|T,
5605_C|T, 5626_G|T, 5639_C|T, 5641_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5689_A|G, 5692_T|C, 5701_T|A, 5708_T|C, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_CC|GT, 5740_G|A, 5749_A|G, 5758_G|A,
5760_G|A, 5764_A|G, 5773_G|A, 5776_A|T, 5779_G|A, 5797_T|C, 5800_A|C, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A,
5935_A|C, 5938_C|T, 5941_T|C, 5947_T|C, 5953_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6007_T|C, 6013_T|A, 6023_A|G,
6025_T|C, 6031_C|T, 6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6067_G|A, 6100_C|T, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6142_T|A, 6145_T|C, 6154_AC|GT, 6157_G|A,
6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6229_A|G, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6280_C|T, 6283_T|A, 6292_T|C, 6295_G|A, 6310_C|T,
6316_A|G, 6334_T|C, 6346_A|G, 6351_A|G, 6356_C|T, 6361_C|G, 6367_G|A, 6373_T|C, 6379_A|G, 6385_G|T, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6445_T|G, 6448_T|A, 6451_A|G, 6463_G|A, 6478_T|A, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_CC|GA, 6547_C|T, 6550_T|C, 6569_C|T,
6571_A|G, 6595_A|G, 6611_A|G, 6613_A|T, 6616_G|A, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|A, 6673_T|C, 6676_A|G, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6709_T|C, 6715_T|C,
6724_C|T, 6730_A|G, 6733_C|T, 6745_T|C, 6757_TG|CA, 6766_C|G, 6772_C|T, 6781_G|A, 6790_T|G, 6793_GA|AG, 6796_C|T, 6799_C|A, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6829_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6859_C|T, 6863_A|G, 6874_A|C, 6876_C|T, 6889_C|T, 6892_G|A, 6895_A|G, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6952_T|C, 6955_TG|CA, 6958_TT|CG, 6969_G|A, 6976_G|A, 6986_C|T, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G, 7030_A|G, 7046_T|C,
7054_C|T, 7063_A|G, 7066_C|T, 7069_A|G, 7079_C|T, 7084_T|C, 7096_A|T, 7105_A|G, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|C, 7174_G|A, 7178_G|A, 7180_C|T,
7186_C|A, 7211_C|T, 7216_C|T, 7225_A|T, 7228_G|A, 7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7279_G|A, 7286_C|T, 7288_T|G, 7291_A|C, 7297_A|G, 7300_G|A, 7312_C|T,
7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7366_T|C, 7369_T|G, 7378_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7426_CC|TT, 7429_A|G,
7432_T|C, 7450_A|G, 7453_G|C, 7456_C|T, 7465_G|A, 7468_T|C, 7480_CC|AT, 7483_A|G, 7492_T|A, 7495_CT|TC, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7519_C|T, 7528_T|C, 7531_T|G, 7552_C|G,
7561_A|G, 7571_A|C, 7576_G|T, 7580_C|T, 7582_C|T, 7597_A|T, 7612_A|C, 7630_A|G, 7634_C|A, 7642_C|A, 7645_G|A, 7651_A|G, 7660_G|A, 7666_A|G, 7675_G|A, 7687_T|C, 7691_T|C, 7696_C|T, 7701_G|A,
7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|A, 7753_G|A, 7762_G|A, 7765_TT|CC, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7813_C|T, 7816_A|C, 7819_G|A, 7822_A|G, 7825_G|A,
7831_C|T, 7837_G|A, 7851_A|G, 7855_G|T, 7861_T|C, 7869_T|C, 7876_G|A, 7879_G|A, 7882_T|C, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_T|C, 8011_C|T, 8014_C|T, 8023_A|G, 8041_A|G, 8044_A|G, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8089_AT|TC, 8092_G|A, 8095_A|G,
8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C, 8131_T|C, 8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_G|T, 8154_C|G, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T, 8188_A|G, 8209_T|G,
8212_C|A, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8248_A|G, 8251_A|G, 8254_G|C, 8260_G|A, 8266_T|C, 8269_C|T, 8275_G|A, 8278_T|C, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8302_G|A,
8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G, 8354_C|T, 8356_G|A, 8362_G|A, 8374_T|C, 8380_T|A, 8383_A|C, 8392_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A,
8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_ATGA|GCAG, 8510_T|A, 8512_T|C, 8518_TT|CC, 8524_C|T, 8533_C|T, 8539_C|T, 8551_C|T, 8554_C|T, 8574_A|G,
8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G, 8614_T|C, 8617_A|G, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8707_A|G,
8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8792_C|T, 8797_C|T, 8800_A|G, 8808_A|G, 8815_A|G, 8824_A|G, 8830_A|G, 8833_A|G, 8839_T|A, 8851_A|C, 8854_T|C, 8874_A|T,
8923_C|T, 8929_G|A, 8938_AC|GT, 8954_A|C, 8957_AA|CG, 8962_G|A, 8965_C|T, 8968_A|G, 8971_A|G, 8974_C|T, 8986_T|C, 9019_G|A, 9022_G|A, 9034_T|C, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T,
9055_T|C, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9177_A|C, 9179_T|C,
9187_A|C, 9190_T|C, 9212_A|C, 9214_G|A, 9217_T|A, 9232_C|T, 9235_G|A, 9244_C|A, 9259_G|A, 9268_A|G, 9274_A|G, 9277_C|T, 9280_T|G, 9299_T|C, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G,
9335_CAA|TTG, 9343_G|A, 9361_G|A, 9367_A|G, 9379_G|C, 9382_G|A, 9391_C|A, 9397_A|T, 9406_C|A, 9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G, 9445_C|T, 9467_C|T, 9485_T|C, 9490_A|G, 9496_AT|GC,
9505_A|G, 9527_A|G, 9529_A|T, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG, 9562_A|G, 9571_C|A, 9573_GG|AA, 9577_G|C, 9590_A|G, 9598_C|T, 9601_A|G, 9607_C|T,
9610_AC|GT, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9691_C|T, 9709_TA|GC, 9712_A|C, 9718_C|T, 9745_G|A, 9754_T|C, 9769_C|G, 9775_T|C, 9790_T|C,
9796_A|G, 9799_G|A, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T, 9883_C|T, 9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A, 9916_A|G,
9919_C|T, 9938_C|T, 9946_T|C, 9949_T|C, 9955_A|G, 9961_C|T, 9970_A|G, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10024_C|T, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G,
10051_G|A, 10063_C|T, 10066_G|A, 10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_TC|CT, 10165_A|G, 10174_A|G, 10177_A|G,
10186_G|T, 10189_C|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10294_C|T,
10297_A|G, 10309_C|T, 10312_G|A, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10365_AA|TG, 10369_10377, 10383_10385, 10391_10394, 10396_10398, 10403_10405,
10407, 10409_10411, 10412_C|G, 10416_10417, 10418_C|T, 10421_10429, 10434_10442, 10445_10446, 10450, 10451_C|T, 10455_10460, 10462, 10465_10475, 10522, 10524_G|A, 10526_C|T, 10533_A|G,
10535_T|A, 10550_C|T, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10620_A|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10740_A|G, 10742_T|A, 10847_C|A

Case 3 (A.1): PQ186350.1


Target: 835 samples Number of changes: 1472
BC: A.1 + A.1 BC BR: 1455-1456 BC BR coord: 10527 - 10528
Direction L1: >> Initial region span: 1-1424,1469-1472Gap history (edge excluded): 1424-1469
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 8.03e-03
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1424 183.772526 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1469 1.187284 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 166_A|T, 171_G|A, 197_A|G, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_G|A, 320_T|C, 327_A|G,
346_A|G, 349_C|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 388_T|C, 400_A|T, 409_A|G, 421_T|A, 425_C|T, 430_T|A, 433_TC|CT, 442_G|T, 448_C|T, 454_T|C, 467_T|C, 475_G|T, 488_T|C, 496_G|C, 499_A|G,
501_A|G, 514_CC|TT, 517_A|G, 523_G|C, 535_C|T, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 628_T|C, 634_T|C, 649_G|A,
652_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCTAGAAG, 757_C|T, 760_G|A, 763_T|C,
766_G|A, 790_C|T, 802_A|G, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 877_A|G, 883_G|A, 886, 890_G|T, 891_.|G, 892_C|T, 898_C|T, 901_CC|TT, 904_T|G,
910_A|G, 931_C|T, 940_CC|TT, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 967_C|T, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|T, 1072_T|G, 1090_T|C, 1102_C|A,
1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1165_TC|CT, 1168_C|G, 1183_T|C, 1189_C|T, 1195_C|T, 1204_T|C, 1207_A|T, 1210_G|A, 1216_CC|TT, 1219_A|G, 1228_G|A,
1234_A|G, 1237_G|A, 1240_CA|TC, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G, 1282_T|C, 1285_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1333_T|C, 1339_C|T,
1342_A|G, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1433_A|G, 1435_C|T, 1438_C|T, 1453_G|A, 1471_C|T, 1474_C|T, 1480_A|G,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1544_G|A, 1546_T|C, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G,
1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1606_G|A, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A,
1723_G|A, 1732_CT|TC, 1738_A|G, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1782_A|G, 1785_A|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C, 1819_T|A, 1822_C|T, 1855_G|A,
1858_A|G, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1879_C|T, 1887_T|C, 1900_C|T, 1909_C|T, 1915_C|A, 1926_TT|CC, 1946_T|C, 1969_T|C, 1978_A|G, 1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C,
2020_G|A, 2023_T|A, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2047_C|T, 2053_T|G, 2059_A|G, 2063_C|T, 2080_A|T, 2083_T|C, 2086_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2112_G|C,
2116_A|G, 2119_T|C, 2122_A|T, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G, 2188_A|G, 2193_T|C, 2197_A|G, 2209_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|T, 2230_T|C, 2239_C|T, 2248_G|A,
2251_C|T, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2269_A|G, 2275_T|A, 2278_T|C, 2280_C|T, 2305_G|A, 2308_A|G, 2314_C|T, 2318_T|C, 2322_AC|GT, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G,
2395_C|T, 2408_T|C, 2413_A|T, 2418_TG|CC, 2432_T|C, 2437_T|C, 2446_T|G, 2452_G|A, 2455_T|C, 2464_C|T, 2467_C|A, 2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2515_A|C,
2518_T|C, 2521_A|G, 2524_C|T, 2527_T|G, 2533_C|T, 2548_C|T, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|C, 2593_A|G, 2599_T|C, 2602_T|C, 2605_A|G, 2620_CC|TT, 2626_T|C, 2632_T|C, 2635_C|T, 2641_T|G,
2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2677_C|T, 2686_TT|CC, 2698_C|T, 2701_G|A, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_T|C, 2731_A|C, 2734_G|A,
2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|T, 2776_G|T, 2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2827_C|T, 2833_G|A, 2836_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2887_T|C,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 3007_T|G, 3013_G|A, 3019_C|T, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C,
3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G, 3271_A|G, 3289_T|C, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|TGG, 3328_T|C, 3334_G|T, 3337_A|G, 3349_A|G,
3358_G|C, 3364_C|T, 3370_AG|GA, 3382_A|G, 3394_C|A, 3397_C|A, 3400_C|T, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3480_G|A,
3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G, 3511_A|G, 3514_AA|GG, 3517_A|C, 3523_T|A, 3535_TT|GC, 3566_G|T, 3569_C|T, 3571_A|G, 3573_G|A, 3577_A|G, 3589_A|C, 3598_G|A, 3610_AG|CA, 3620_T|C,
3622_G|A, 3628_A|C, 3632_C|T, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3658_T|C, 3667_A|G, 3670_CAC|TGT, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T,
3715_A|G, 3718_C|T, 3727_T|C, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3751_A|G, 3757_A|G, 3760_A|G, 3763_G|A, 3769_C|T, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3814_T|A, 3820_G|A, 3826_A|G,
3832_A|C, 3835_C|T, 3847_T|A, 3856_T|C, 3860_G|A, 3868_C|A, 3871_C|G, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3940_A|G, 3945_ATA|GCG,
3949_C|A, 3953_T|C, 3959_C|T, 3961_C|G, 3967_T|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4009_A|G, 4013_T|C, 4018_T|C, 4021_TG|CA, 4030_T|C, 4036_A|C, 4045_T|C, 4054_T|C, 4056_TC|CA, 4066_C|T,
4075_G|A, 4081_T|C, 4087_T|C, 4105_C|G, 4108_A|T, 4120_C|A, 4129_A|G, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4204_C|T, 4210_A|G, 4219_A|C, 4229_C|T,
4231_G|A, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|G, 4270_T|C, 4274_A|G, 4289_C|A, 4291_C|T, 4304_G|A, 4306_T|C, 4321_G|A, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4360_A|T,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4411_A|T, 4423_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4444_T|C, 4447_A|G, 4450_G|A, 4453_A|G, 4456_G|T, 4465_C|T, 4469_G|A,
4474_G|C, 4489_C|T, 4495_T|C, 4498_G|A, 4501_T|C, 4504_CC|TA, 4519_T|G, 4522_TC|CA, 4531_C|T, 4540_G|T, 4544_C|T, 4547_T|C, 4549_T|C, 4557_G|A, 4561_A|G, 4576_G|A, 4579_T|C, 4583_T|C,
4585_G|C, 4594_T|C, 4597_CA|TG, 4600_T|A, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G, 4627_TC|CT, 4630_G|A, 4639_G|A, 4651_A|T, 4660_A|G, 4663_C|T, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A,
4684_A|G, 4711_G|C, 4720_A|G, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4753_C|T, 4756_G|A, 4769_T|C, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4792_A|C, 4795_G|A, 4813_T|C, 4819_C|T, 4829_T|C,
4840_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4891_C|T, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4924_C|T, 4927_A|G, 4930_G|T,
4939_G|C, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4981_T|C, 4987_A|C, 4993_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5014_G|A, 5020_T|A, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5103_A|G, 5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A, 5140_A|G, 5152_TG|AA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|G, 5176_T|C,
5179_G|A, 5182_G|A, 5185_A|T, 5188_A|G, 5191_T|C, 5194_C|T, 5197_C|T, 5200_A|T, 5206_CT|TC, 5212_C|T, 5215_G|A, 5218_C|T, 5230_CT|GC, 5239_T|G, 5245_GT|TC, 5251_C|T, 5257_C|T, 5269_T|C,
5272_T|C, 5275_A|G, 5287_T|C, 5293_C|T, 5299_G|A, 5302_C|T, 5305_G|A, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G, 5335_C|T, 5344_G|A, 5346_GA|AG, 5368_C|T, 5371_T|C, 5374_C|T, 5380_A|G,
5383_T|A, 5389_G|A, 5393_T|C, 5398_A|G, 5407_G|A, 5410_T|G, 5413_T|G, 5416_C|T, 5422_A|G, 5431_T|C, 5440_A|G, 5443_C|T, 5452_G|A, 5458_A|G, 5461_T|C, 5470_C|A, 5479_T|C, 5488_G|A, 5491_C|T,
5500_G|A, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5602_A|T, 5605_C|T, 5623_A|G, 5626_G|T, 5639_C|T, 5641_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5689_A|G,
5692_T|C, 5701_T|A, 5707_TT|CC, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_CC|GT, 5740_G|A, 5749_A|G, 5758_G|A, 5760_G|A, 5764_A|G, 5773_G|A, 5776_A|T, 5779_G|A, 5788_A|G, 5797_T|C,
5800_A|C, 5806_C|T, 5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5857_T|C, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5953_G|A,
5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6013_T|A, 6023_A|G, 6025_T|C, 6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6067_G|A,
6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6142_T|G, 6145_T|C, 6154_AC|GT, 6157_G|A, 6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6229_A|G, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|A, 6286_G|A, 6292_T|C, 6310_C|T, 6316_A|G, 6322_G|A, 6328_C|T, 6334_T|C, 6346_A|G, 6351_A|G, 6361_C|G,
6367_G|A, 6373_T|C, 6379_A|G, 6385_G|T, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6445_T|G, 6448_T|A, 6451_A|G,
6457_A|G, 6478_T|A, 6490_T|C, 6493_A|G, 6499_T|C, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6529_CC|TT, 6532_CC|GA, 6547_C|T, 6550_T|C, 6571_A|G, 6595_A|G, 6611_A|G, 6613_A|T, 6622_AC|GT,
6625_A|G, 6634_G|T, 6643_C|T, 6667_C|A, 6673_T|C, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6709_T|C, 6715_T|C, 6724_C|T, 6730_A|G, 6733_C|T, 6736_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|G,
6769_A|C, 6772_C|T, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6802_G|A, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6850_T|C, 6859_C|T, 6871_T|C,
6874_A|C, 6876_C|T, 6883_A|G, 6889_C|T, 6892_G|A, 6895_A|G, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T, 6934_G|A, 6940_C|T, 6943_A|G, 6952_T|C, 6955_TG|CA, 6958_TT|CG,
6969_GT|AC, 6976_G|A, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G, 7030_A|G, 7036_C|T, 7046_T|C, 7054_C|T, 7063_A|G, 7066_C|T, 7069_A|G, 7079_C|T, 7081_G|A, 7084_T|C, 7096_A|T,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7171_G|C, 7174_G|A, 7177_GG|AA, 7180_C|T, 7211_C|T, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A,
7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7273_G|A, 7279_G|A, 7286_C|T, 7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7369_T|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7438_T|A, 7450_A|G, 7453_G|C, 7456_C|T, 7465_G|A, 7468_T|C,
7480_CC|AT, 7483_A|G, 7492_T|A, 7495_C|T, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7519_C|T, 7528_T|C, 7531_T|A, 7552_C|G, 7561_A|G, 7564_A|G, 7571_A|C, 7580_C|T, 7582_C|T, 7597_A|T, 7612_A|C,
7627_T|C, 7630_A|G, 7634_C|A, 7642_C|A, 7645_G|A, 7651_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|A, 7753_G|A,
7762_G|A, 7765_T|C, 7771_C|T, 7789_C|T, 7798_G|T, 7804_C|G, 7807_G|A, 7813_C|T, 7816_A|T, 7819_G|A, 7822_A|G, 7825_G|A, 7831_C|T, 7837_G|A, 7855_G|A, 7861_T|C, 7869_T|C, 7876_G|A, 7879_G|A,
7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7939_A|G, 7942_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_T|C, 8011_C|T, 8014_C|T,
8023_A|G, 8041_A|G, 8044_A|G, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8087_A|G, 8088_.|CTC, 8096_T|G, 8099_8101, 8104_A|C, 8120_G|A, 8123_A|C, 8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G,
8145_A|G, 8152_G|T, 8154_C|G, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T, 8188_A|G, 8209_T|G, 8212_C|A, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8248_A|G, 8251_A|G, 8254_G|C, 8260_G|A,
8266_T|C, 8269_C|T, 8275_G|A, 8278_T|C, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8302_G|A, 8305_T|C, 8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G, 8354_C|T, 8362_GA|AC,
8374_T|C, 8380_T|A, 8383_A|C, 8392_C|T, 8422_G|A, 8434_T|G, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|C, 8476_A|G, 8485_G|A, 8488_G|A, 8505_TGA|CAG,
8510_T|A, 8518_TT|CC, 8551_C|T, 8554_C|T, 8557_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G, 8614_T|C, 8617_A|G, 8629_T|C, 8632_A|C, 8638_C|T,
8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8785_C|T, 8800_A|G, 8815_A|G, 8824_A|G,
8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|C, 8854_T|C, 8863_C|T, 8866_T|C, 8874_A|T, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8962_G|A, 8968_A|G, 8971_A|G, 8974_C|T,
9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A, 9127_T|C, 9133_T|A,
9136_C|T, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9187_A|C, 9190_T|C, 9212_A|C, 9214_G|A, 9217_T|A, 9232_C|T, 9235_G|T, 9244_C|A, 9259_G|A, 9274_A|G,
9277_C|T, 9280_T|G, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G, 9335_CAA|TTG, 9343_G|A, 9361_G|A, 9367_A|G, 9379_G|C, 9382_G|A, 9391_C|A, 9397_A|T, 9400_G|A, 9403_A|G, 9406_C|A,
9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G, 9445_C|T, 9467_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9505_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG,
9562_A|G, 9571_C|A, 9573_GG|AA, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C, 9610_AC|GT, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9691_C|T, 9709_TA|GC,
9712_A|C, 9745_G|A, 9754_T|C, 9769_C|G, 9772_C|T, 9775_T|C, 9790_T|C, 9796_A|G, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|C, 9841_G|A, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T,
9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A, 9916_A|G, 9919_C|T, 9938_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10024_C|T, 10027_A|C,
10030_A|G, 10036_GA|TG, 10042_T|C, 10051_G|A, 10066_G|A, 10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C,
10174_A|G, 10186_G|T, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_GC|AT, 10273_AC|GA, 10276_G|A,
10294_C|T, 10297_A|G, 10312_G|A, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10363_C|T, 10365_A|T, 10369_10377, 10381_10382, 10385, 10391_10397,
10403_10405, 10407, 10409_10411, 10412_C|G, 10416_10417, 10418_C|T, 10421_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10462, 10465_10475, 10522, 10524_G|A, 10526_C|T,
10528_G|A, 10533_A|G, 10535_T|A, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T, 10620_A|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|CA, 10681_C|T, 10703_C|T,
10740_A|G, 10847_C|A

Case 3 (A.1): PQ186354.1


Target: 835 samples Number of changes: 1460
BC: A.1 + A.1 BC BR: 1439-1440 BC BR coord: 10468 - 10469
Direction L1: >> Initial region span: 1-1416,1456-1460Gap history (edge excluded): 1416-1456
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.30e-13
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1416 186.632879 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1456 1.211665 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 130_T|C, 171_G|A, 177_TT|CC, 247_T|C, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C, 327_AA|GG, 346_A|G, 349_C|A,
352_G|A, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 400_A|C, 409_A|G, 421_T|A, 430_T|A, 433_TC|CT, 442_G|T, 448_C|T, 451_A|G, 454_TT|CC, 466_GT|AC, 475_G|T, 488_T|C, 490_G|A, 496_G|C, 499_A|G,
501_A|G, 515_C|T, 517_A|G, 523_G|C, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 622_C|T, 628_T|C, 634_T|C, 637_C|T,
649_G|A, 655_A|T, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|T, 754_T|C, 763_T|C, 766_G|A, 775_C|T, 799_A|G,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 874_T|C, 883_G|A, 886_T|C, 889_GA|AG, 892_C|T, 898_C|T, 901_CC|TT, 904_T|A, 910_A|G,
931_C|T, 941_C|T, 949_C|T, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 1036_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|T, 1072_T|G, 1090_T|C, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1158_A|G, 1162_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1183_T|C, 1189_C|T, 1204_T|C, 1207_A|T, 1216_CC|TT, 1219_A|G, 1222_T|C, 1228_G|A, 1234_A|G,
1237_G|A, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1267_T|C, 1279_C|G, 1285_C|T, 1294_A|G, 1298, 1306_.|A, 1321_C|T, 1327_A|G, 1333_T|C, 1342_A|G, 1351_TT|CC, 1366_T|C, 1378_T|C,
1387_C|T, 1393_A|G, 1400_T|C, 1408_A|T, 1411_G|A, 1423_A|G, 1426_T|C, 1432_TA|CG, 1435_C|T, 1441_T|C, 1447_T|C, 1453_G|A, 1474_C|T, 1480_A|G, 1482_TC|CT, 1486_G|A, 1491_T|C, 1495_G|A,
1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1522_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1544_G|A, 1546_T|C, 1549_C|T, 1552_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T,
1606_G|A, 1609_C|T, 1618_G|A, 1621_A|T, 1642_G|T, 1669_C|G, 1672_A|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1723_G|A, 1732_C|T, 1747_T|C,
1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1777_A|C, 1782_A|G, 1785_A|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1819_T|A, 1822_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T,
1879_C|T, 1887_T|C, 1894_C|G, 1915_C|A, 1924_T|C, 1926_TT|CC, 1946_T|C, 1969_T|C, 1978_A|G, 1981_A|G, 1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2047_C|T, 2053_T|G, 2063_C|T, 2080_A|C, 2083_T|C, 2086_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2119_T|C, 2122_A|T, 2125_T|C, 2128_C|G, 2131_T|C,
2146_A|G, 2152_A|C, 2164_A|G, 2168_T|C, 2188_A|G, 2193_T|C, 2197_A|G, 2201_C|T, 2209_C|T, 2215_A|G, 2218_CA|TG, 2230_T|C, 2239_C|T, 2248_G|A, 2251_C|T, 2254_C|T, 2257_T|A, 2260_G|A, 2266_G|A,
2275_T|A, 2278_T|C, 2280_C|T, 2299_T|C, 2302_G|A, 2305_GC|AT, 2308_A|G, 2314_C|T, 2322_AC|GT, 2335_G|A, 2344_G|T, 2350_G|A, 2353_A|C, 2376_CA|TG, 2380_A|G, 2395_C|T, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2467_C|A, 2479_C|T, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_TA|AG, 2509_C|T, 2515_A|C, 2521_A|G, 2524_C|T, 2527_T|A, 2533_C|T,
2548_C|T, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|T, 2593_A|G, 2599_T|C, 2602_T|C, 2620_CC|TT, 2626_T|C, 2632_T|C, 2638_C|T, 2641_T|G, 2644_G|A, 2650_G|A, 2659_A|G, 2668_A|G, 2686_TT|CC,
2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_T|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2752_A|G, 2755_T|A, 2761_A|T, 2764_T|C, 2776_G|T,
2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2824_C|T, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2926_T|C, 2947_A|T, 2950_C|A, 2962_C|T,
2983_A|G, 2986_C|T, 3007_T|G, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G,
3121_G|A, 3127_G|A, 3133_AC|GT, 3142_T|C, 3157_A|C, 3169_T|C, 3172_A|C, 3187_A|G, 3199_C|T, 3205_T|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G,
3265_A|G, 3271_A|G, 3289_T|C, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3313_T|C, 3316_T|C, 3319_CAAC|TGGT, 3328_T|C, 3331_A|G, 3334_G|T, 3349_A|G, 3358_G|C, 3361_T|C, 3364_C|T,
3370_AG|GA, 3382_A|G, 3394_C|A, 3397_C|A, 3400_C|T, 3412_T|A, 3421_C|T, 3427_T|G, 3436_G|T, 3439_T|C, 3460_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3480_G|A, 3484_T|C, 3490_G|T, 3496_C|A, 3502_T|G,
3514_AA|GG, 3517_A|C, 3523_T|A, 3529_T|C, 3535_TT|GC, 3569_C|T, 3573_G|A, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3610_AG|CA, 3620_T|C, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3667_A|G, 3673_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3721_C|T, 3727_T|C, 3733_GT|CC, 3739_T|C,
3745_C|T, 3757_A|G, 3763_G|A, 3778_T|C, 3782_C|T, 3784_C|G, 3790_C|A, 3793_A|G, 3802_T|C, 3820_G|A, 3826_A|G, 3832_A|T, 3847_T|A, 3851_T|C, 3856_T|C, 3860_G|A, 3868_C|A, 3871_CC|GT, 3883_T|C,
3895_T|G, 3898_T|C, 3908_C|T, 3928_T|C, 3931_TA|CC, 3934_G|A, 3946_T|C, 3949_C|T, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3967_TC|GT, 3982_C|G, 3985_T|A, 3998_A|C, 4006_CG|AA, 4009_A|G,
4013_T|C, 4021_TG|CA, 4030_T|C, 4036_A|C, 4045_T|C, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4096_C|T, 4099_C|T, 4105_C|G, 4108_A|T, 4117_G|A, 4120_C|A, 4129_A|G, 4142_C|T,
4150_A|C, 4153_TC|CA, 4165_C|A, 4168_A|G, 4171_T|C, 4174_G|A, 4183_T|C, 4198_G|A, 4204_C|T, 4210_A|G, 4216_T|C, 4219_A|C, 4234_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|G, 4270_T|C,
4274_A|G, 4285_A|G, 4289_C|A, 4291_C|T, 4303_G|A, 4306_T|C, 4321_G|A, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A, 4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T,
4399_C|T, 4411_A|T, 4423_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4456_G|T, 4465_C|T, 4469_G|A, 4474_G|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4507_C|T, 4516_T|C,
4519_T|A, 4522_TC|CA, 4531_C|T, 4547_T|C, 4557_G|A, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G, 4600_T|A, 4603_T|C, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G, 4628_C|T,
4630_G|A, 4639_G|A, 4651_A|T, 4663_C|T, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4711_G|C, 4720_A|G, 4732_C|G, 4741_A|T, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4769_T|C,
4771_GA|AG, 4774_T|C, 4778_T|A, 4792_A|C, 4798_A|G, 4819_C|T, 4829_T|C, 4831_G|A, 4849_A|G, 4852_G|A, 4855_A|G, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4890_A|G, 4900_C|T,
4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|C, 4954_T|G, 4957_C|G, 4969_T|C, 4975_T|C, 4978_C|T, 4981_T|C, 4984_A|C, 4987_A|C, 4993_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5014_G|A, 5020_T|A, 5024_C|T, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5101_A|G, 5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A,
5152_TG|CA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|G, 5176_T|C, 5185_A|T, 5191_T|C, 5194_C|T, 5200_A|C, 5206_CT|TC, 5209_G|A, 5212_C|T, 5215_G|A, 5230_CT|GC, 5239_T|A, 5245_GT|TC, 5251_C|T,
5257_C|T, 5260_G|A, 5269_T|C, 5272_T|C, 5275_A|G, 5281_G|A, 5287_T|C, 5302_C|T, 5305_G|A, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5332_T|G, 5335_C|T, 5344_G|A, 5353_C|T, 5368_C|T, 5380_A|G,
5383_T|A, 5393_T|C, 5401_A|G, 5407_G|A, 5410_T|G, 5413_T|A, 5416_C|T, 5428_C|T, 5431_T|C, 5440_A|G, 5443_C|T, 5449_T|C, 5452_G|A, 5458_A|G, 5461_T|C, 5470_C|A, 5473_T|C, 5488_G|A, 5500_G|A,
5509_A|G, 5530_A|T, 5539_G|T, 5542_T|A, 5545_G|A, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T, 5602_A|T, 5619_A|G, 5623_A|G, 5626_G|T, 5639_C|T, 5641_A|G, 5647_C|T, 5662_A|C,
5668_C|T, 5683_A|G, 5689_A|G, 5692_T|C, 5701_T|A, 5708_T|C, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_C|G, 5740_G|A, 5749_A|G, 5758_G|A, 5760_G|A, 5764_A|G, 5767_C|T, 5773_G|A, 5776_A|C,
5779_G|A, 5788_A|G, 5797_T|C, 5800_A|C, 5827_A|G, 5836_T|C, 5839_C|T, 5846_C|A, 5857_T|C, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5932_C|A, 5935_A|C, 5938_C|T, 5941_T|C,
5947_T|C, 5953_G|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6013_T|A, 6023_A|G, 6025_T|C, 6034_C|T, 6037_C|T, 6047_T|C,
6052_G|A, 6058_A|G, 6065_T|C, 6100_C|A, 6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6142_T|G, 6145_T|C, 6154_AC|GT, 6157_G|A, 6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C,
6187_A|G, 6199_T|C, 6208_G|T, 6211_C|T, 6220_T|C, 6223_G|A, 6229_A|G, 6235_C|T, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|A, 6292_T|C, 6310_C|T, 6316_A|G, 6322_G|A,
6334_T|C, 6346_A|G, 6351_A|G, 6355_T|C, 6359_C|A, 6361_C|G, 6373_T|C, 6379_A|G, 6385_G|T, 6391_T|C, 6400_T|C, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6433_T|C, 6439_G|A, 6442_A|G,
6445_T|G, 6448_T|A, 6451_A|G, 6457_A|G, 6463_G|A, 6478_T|A, 6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_CC|GA, 6535_C|T, 6547_C|T, 6550_T|C, 6569_C|T, 6571_A|G,
6595_A|G, 6611_A|G, 6613_A|T, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|A, 6673_T|C, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6733_C|T, 6745_T|C,
6757_TG|CA, 6766_C|A, 6772_C|T, 6790_T|G, 6794_A|G, 6796_C|T, 6799_C|A, 6805_A|G, 6808_G|A, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6835_A|G, 6841_A|T, 6844_C|T, 6850_T|C,
6856_C|T, 6859_CC|TA, 6866_C|T, 6874_A|T, 6876_C|T, 6883_A|G, 6889_C|T, 6892_G|A, 6895_A|G, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6925_C|T, 6931_G|A, 6934_G|A, 6936_A|G, 6940_C|T,
6943_A|G, 6953_A|G, 6955_TG|CA, 6958_TT|CG, 6969_G|A, 6976_G|A, 6986_C|T, 6988_G|A, 6997_A|G, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|G, 7036_C|T, 7039_T|C, 7046_T|C, 7054_C|T,
7063_A|G, 7066_C|T, 7069_A|G, 7084_T|C, 7096_A|T, 7114_CC|TT, 7117_T|A, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7156_T|C, 7159_C|T, 7171_G|C, 7174_G|A, 7177_GG|AA, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7270_A|G, 7273_G|A, 7279_G|A, 7286_C|T, 7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A,
7324_C|T, 7327_T|A, 7339_G|A, 7350_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7408_T|C, 7412_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7426_C|T, 7429_A|G, 7432_T|C, 7450_A|G,
7453_G|C, 7456_C|T, 7465_G|A, 7468_T|C, 7480_CC|GT, 7492_T|A, 7495_CT|TC, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G, 7519_C|T, 7531_T|G, 7552_C|A, 7571_A|C, 7580_C|T, 7597_A|T, 7612_A|C,
7630_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7657_T|C, 7666_A|G, 7675_G|A, 7681_A|G, 7687_TC|CT, 7691_T|C, 7701_G|A, 7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|G, 7753_G|A, 7759_C|T,
7762_G|A, 7765_TT|CC, 7771_C|T, 7789_C|T, 7798_G|T, 7804_C|T, 7807_G|A, 7813_C|T, 7816_A|T, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7855_G|A, 7858_A|G, 7861_T|C, 7869_T|C, 7874_C|T,
7876_G|A, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7924_A|G, 7936_C|T, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_TC|CT,
8011_C|T, 8014_C|T, 8023_A|G, 8029_T|C, 8039_C|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C,
8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_G|T, 8154_C|G, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T, 8188_A|G, 8209_T|G, 8212_C|T, 8218_AC|GT, 8224_A|G, 8227_G|A, 8245_C|T, 8248_A|G,
8251_A|G, 8254_G|C, 8260_G|A, 8266_T|C, 8275_G|A, 8278_T|C, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8302_G|A, 8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G, 8354_C|T, 8356_G|A, 8362_G|A,
8374_T|C, 8380_T|A, 8383_A|C, 8392_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A, 8449_A|G, 8452_C|A, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|C, 8476_A|G, 8485_G|A, 8488_G|A,
8500_G|A, 8505_T|C, 8507_A|G, 8510_T|A, 8512_T|C, 8519_T|C, 8551_C|T, 8554_C|T, 8557_T|C, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8608_T|A, 8611_T|G, 8617_A|G,
8629_T|C, 8632_A|C, 8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8692_G|A, 8707_A|G, 8743_G|A, 8746_A|C, 8749_T|C, 8752_G|A, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8792_C|T, 8797_C|T, 8800_A|G,
8808_A|G, 8815_AC|GT, 8824_A|T, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8851_A|C, 8854_T|C, 8866_T|C, 8874_A|T, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8962_G|A,
8971_A|G, 8974_C|T, 9007_G|A, 9019_G|A, 9022_G|A, 9034_T|C, 9037_G|A, 9043_A|G, 9046_G|A, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9113_C|T, 9115_G|A,
9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9163_A|G, 9166_C|T, 9169_T|C, 9172_CT|AC, 9175_A|G, 9179_T|C, 9181_C|T, 9187_A|C, 9190_T|C, 9201_A|G, 9212_A|T, 9214_G|A, 9217_T|A, 9232_C|T,
9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9313_C|T, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_A|G, 9335_CAA|TTG, 9340_A|T, 9343_G|A, 9361_G|A, 9367_A|G, 9379_G|C, 9382_G|A,
9397_A|T, 9406_C|A, 9409_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9439_A|G, 9463_T|C, 9466_TC|AT, 9472_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9505_A|G, 9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G,
9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|TG, 9562_A|G, 9566_C|T, 9571_C|A, 9573_G|A, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C, 9607_C|T, 9610_AC|GT, 9625_G|A, 9631_T|C, 9637_C|T,
9646_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9709_TA|GC, 9712_A|C, 9745_G|A, 9754_T|C, 9769_C|G, 9775_T|C, 9790_T|C, 9796_A|G, 9799_G|A, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_C|A, 9856_G|A, 9859_A|G, 9865_G|A, 9868_G|T, 9880_C|T, 9898_A|G, 9904_T|A, 9910_C|A, 9916_A|G, 9919_C|T, 9938_C|T, 9946_T|C, 9955_A|G, 9958_G|A, 9970_A|G, 9977_T|C, 9985_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10021_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10096_A|G, 10103_AC|GT, 10126_C|T, 10129_G|A, 10132_A|G, 10134_TG|CA,
10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10174_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10213_T|C, 10222_C|T, 10228_C|A, 10231_C|T, 10234_C|T, 10237_C|T,
10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_GC|AT, 10273_AC|GA, 10276_G|T, 10291_C|T, 10294_C|T, 10297_A|G, 10309_C|T, 10312_G|A, 10315_T|C,
10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10355_A|G, 10363_C|T, 10365_AA|TG, 10369_10377, 10381_10382, 10385, 10391_10397, 10402_10410, 10414, 10418_10422, 10425_C|T, 10427_10429,
10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10464_10475, 10522, 10524_G|A, 10526_C|T, 10533_A|G, 10535_T|G, 10550_C|G, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|T,
10620_A|C, 10635_G|A, 10639_C|T, 10647_C|T, 10658_.|C, 10659_AG|TA, 10681_C|T, 10738_C|T, 10817_T|C, 10847_C|A

Case 3 (A.1): PQ441955.1


Target: 835 samples Number of changes: 1437
BC: A.1.NmC2 + A.1 BC BR: 11-12 BC BR coord: 280 - 281
Direction L1: << Initial region span: 1-9,1412-1437Gap history (edge excluded): 9-1412
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 9.54e-02
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 9 2.616115 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1412 8.011651 None None None * * *



Target sequence

, 108_C|T, 118_C|A, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 271_T|C, 280_CA|TG, 289_T|C, 295_A|G, 304_A|T, 307_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 358_T|C, 361_A|G, 363_G|A, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 446_T|C, 448_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 496_G|C, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 550_C|T, 556_G|T, 559_C|T, 565_C|T, 577_A|C, 584_T|C, 589_A|G, 610_C|T, 613_A|C, 628_T|C, 631_C|T, 649_G|A, 655_A|T,
664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCCAGAAG, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G,
811_T|C, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 859_G|A, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 916_C|T,
931_C|T, 934_G|C, 937_T|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1181_A|G, 1183_T|C, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|C, 1249_C|T, 1255_C|A, 1261_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1288_T|C, 1294_A|G, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1433_A|G, 1435_C|T, 1441_T|C, 1444_G|A, 1462_C|T, 1465_G|T, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1501_A|G, 1504_A|G, 1507_T|C, 1510_A|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A,
1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1714_G|T,
1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1760_A|C, 1762_G|A, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1804_T|C, 1807_T|G, 1810_A|G, 1813_T|C, 1819_T|G,
1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|A, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_TT|CC, 1900_C|T, 1915_C|A, 1921_C|T, 1926_TT|CA, 1936_G|A, 1942_A|G,
1946_T|C, 1951_A|G, 1957_C|G, 1969_T|C, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2050_T|C,
2063_C|T, 2068_T|C, 2080_A|T, 2083_T|C, 2089_A|G, 2098_C|T, 2101_T|C, 2104_C|A, 2110_G|A, 2112_G|C, 2116_A|G, 2119_T|C, 2125_TC|CT, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2188_A|G,
2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2266_G|A, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_GC|AT,
2308_A|G, 2314_C|T, 2322_A|G, 2335_G|A, 2341_C|T, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2554_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2611_G|A, 2621_C|T, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2650_G|A, 2686_TT|CC, 2695_A|G, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2728_TC|CT, 2734_G|A, 2737_TG|CA, 2752_A|G, 2755_T|A, 2761_A|T, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2845_A|G,
2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3086_A|G, 3091_C|T, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3172_A|C, 3184_G|A, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|A, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3370_AG|GA, 3373_T|C, 3376_T|C,
3397_C|A, 3409_G|A, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3490_G|C, 3496_C|A, 3502_T|G,
3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|GT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3601_G|A, 3604_T|C, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A,
3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G,
3718_C|T, 3733_G|C, 3739_T|C, 3745_C|T, 3748_T|C, 3778_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3826_A|G, 3829_A|G, 3832_A|T, 3850_C|T, 3853_G|A, 3860_G|A, 3868_C|A, 3871_C|T,
3883_TC|CT, 3886_A|G, 3895_T|A, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3958_CC|TT, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4054_T|C, 4056_TC|CA, 4061_G|A, 4066_C|T, 4081_T|C, 4105_C|G, 4115_C|T, 4117_G|A, 4120_CT|AC, 4129_A|G, 4132_T|C, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4192_G|A, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A,
4273_GA|AG, 4276_T|C, 4289_C|A, 4304_G|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|A, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4409_G|A, 4411_A|T, 4420_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_GC|AT, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4510_T|C, 4519_T|A, 4522_TC|CT,
4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4561_A|G, 4567_G|A, 4576_G|A, 4583_T|C, 4585_G|T, 4591_T|C, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A,
4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_A|G, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C,
4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4772_A|G, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4865_T|C, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G,
4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4975_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5077_C|T, 5080_G|A, 5092_G|A, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A,
5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5299_G|A, 5305_G|C, 5308_A|G, 5311_C|T, 5323_T|C, 5326_T|C, 5335_C|T, 5338_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5374_C|T,
5378_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5393_T|C, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5443_C|A, 5446_T|C, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5560_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T, 5639_C|T, 5641_A|G,
5644_T|G, 5650_A|G, 5662_A|C, 5668_C|T, 5683_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T,
5839_C|T, 5846_C|A, 5872_T|C, 5875_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C, 5965_T|A, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6004_T|C, 6013_T|C,
6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6043_C|T, 6047_T|C, 6065_T|C, 6067_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G,
6157_G|A, 6160_G|A, 6172_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6205_C|T, 6211_C|T, 6220_T|C, 6223_G|A, 6241_T|C, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A,
6286_G|A, 6299_T|C, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6373_T|C, 6388_A|G, 6403_G|C, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6424_T|C, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6467_A|G, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C,
6553_G|A, 6569_C|T, 6597_T|C, 6611_A|G, 6613_A|T, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6682_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C,
6724_C|T, 6745_T|C, 6757_TG|CA, 6766_C|A, 6772_C|T, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|C,
6844_C|T, 6847_C|T, 6850_T|C, 6860_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6904_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6958_TT|CG,
6964_C|T, 6970_T|C, 6976_G|A, 6979_TC|CT, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7030_A|G, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|A, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7252_C|T, 7255_TT|CC, 7258_A|G, 7288_T|G,
7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|AA, 7324_C|T, 7327_T|G, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7417_T|C, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G,
7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G,
7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7717_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A,
7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7768_G|A, 7771_C|T, 7792_G|A, 7798_G|T, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7861_T|A, 7864_G|A, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A, 7939_A|G, 7945_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7990_T|C, 7996_A|G, 8011_C|T, 8020_C|T, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|TC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC,
8161_G|C, 8167_C|A, 8169_A|G, 8176_T|C, 8185_G|A, 8188_A|G, 8209_T|G, 8212_C|T, 8215_G|A, 8218_A|G, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|T, 8263_C|T, 8272_C|T, 8275_G|A, 8284_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|A, 8320_TG|CA, 8324_A|G, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8401_T|C, 8404_C|T,
8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8504_.|C, 8507, 8510_T|A,
8518_TT|CC, 8524_C|T, 8536_C|T, 8551_C|T, 8554_C|T, 8557_T|C, 8560_C|T, 8574_A|G, 8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C,
8620_TC|CT, 8629_T|C, 8632_A|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8785_C|T, 8788_C|T,
8792_C|T, 8797_C|T, 8801_G|A, 8806_G|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8929_G|A,
8939_C|T, 8941_G|A, 8954_A|C, 8956_GA|AC, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8995_C|T, 9009_9010, 9017_.|AA, 9022_G|A, 9037_G|A, 9043_A|G, 9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C,
9082_G|C, 9085_G|A, 9087_A|T, 9100_G|A, 9103_C|T, 9112_C|T, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9187_A|C, 9190_T|C, 9205_G|A, 9212_A|C, 9214_G|A,
9217_T|G, 9226_A|T, 9229_C|T, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9298_C|T, 9313_C|T, 9317_C|T, 9319_T|C, 9324_AA|GG, 9328_A|G, 9331_G|A, 9334_A|G,
9336_AA|TG, 9340_A|T, 9343_G|A, 9355_A|T, 9361_G|A, 9364_C|T, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9460_T|C, 9463_T|C, 9466_T|C, 9472_C|T, 9475_C|T, 9485_T|C, 9490_A|G, 9497_T|C,
9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_GG|AA, 9577_G|T, 9580_G|A, 9590_AC|GT, 9598_C|T, 9601_A|C,
9604_T|C, 9610_A|G, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9676_G|A, 9679_C|T, 9691_C|T, 9703_C|A, 9709_TA|GC, 9745_G|A, 9749_A|G, 9754_T|C, 9766_G|A, 9769_C|T, 9775_T|C,
9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9844_C|T, 9850_CA|AG, 9856_G|C, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C,
9955_A|G, 9970_A|G, 9973_G|T, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10072_C|T, 10081_G|A, 10096_A|G,
10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10140_AAA|GGG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A,
10222_C|T, 10228_C|A, 10240_TT|CC, 10243_A|G, 10246_C|A, 10249_C|A, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G, 10315_T|C, 10330_C|T, 10336_A|G,
10338_TG|CC, 10348_T|C, 10355_A|G, 10361_10369, 10371_10375, 10378_10387, 10391_10397, 10401_10412, 10417, 10420_10421, 10424_10427, 10430_10437, 10439_10441, 10447_10450, 10452_10454, 10457,
10458_C|T, 10460_C|T, 10463_T|A, 10466_A|G, 10470_G|A, 10475_AGA|TTG, 10512, 10605_AC|CT, 10608_T|C, 10632_C|T, 10635_G|A, 10639_C|T, 10647_C|T, 10658_AG|CC, 10662_.|T, 10681_CT|TC,
10703_C|T

Case 3 (A.1): OP508607.1


Target: 835 samples Number of changes: 612
BC: A.1 + A.1.NmC1 BC BR: 230-231 BC BR coord: 6022 - 6023
Direction L1: << Initial region span: 1-230,231-612Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.25e-88
Rec. model vs L1: 7.12e-30Rec. model vs L2: 5.13e-33
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 231 7.003411 NaN NaN NaN * * *
A.1.NmC1 0 188 2.671382 -35.14282 1744.28564 4.948660e-19
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 231 38.078386 None None None * * *



Target sequence

, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C,
703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G,
841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G,
982_C|T, 985_T|A, 991_T|A, 994_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C,
2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C,
2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A,
2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G,
2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C,
3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 6023_A|G,
6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G,
6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T,
6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T,
6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T,
6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T,
6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T,
7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A,
7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T,
8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A,
8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G,
8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC,
9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C,
9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A,
9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 3 (A.1): OP508611.1


Target: 835 samples Number of changes: 555
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 106-107, 242-243 BC BR coord: 1157 - 1158, 6429 - 6430
Direction L1: << Initial region span: 1-106,107-242,243-555Gap history (edge excluded): 106-243 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.39e-31
Rec. model vs L1: 6.55e-50 Rec. model vs L2: 1.69e-30
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 106 11.446101 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 107 16.053856 NaN NaN NaN * * *
A.1.NmC1 0 243 -0.104244 -58.104191 1644.208382 6.204706e-33
A.1.NmC2 0 243 -0.139336 -104.431540 1736.863079 4.720949e-53
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 243 29.215823 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 943_A|G, 946_G|A, 961_T|C,
964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1915_C|A,
1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_ACC|GTT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A,
5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A,
6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C,
7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC,
8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G,
8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T,
8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T,
9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G,
9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G,
9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T,
9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C,
10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 3 (A.1): OP508620.1


Target: 835 samples Number of changes: 785
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 652-653, 688-689 BC BR coord: 8391 - 8392, 9462 - 9463
Direction L1: >> Initial region span: 1-652,671-688,689-785Gap history (edge excluded): 652-689 -> 652-671
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.91e-11
Rec. model vs L1: 1.33e-18 Rec. model vs L2: 1.75e-21
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 652 19.944874 NaN NaN NaN * * *
A.1.NmC2 0 138 7.172705 -19.69784 2625.39568 9.869578e-23
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 671 1.863676 NaN NaN NaN * * *
A.1.NmC1 0 689 -0.059376 -23.720855 325.441709 1.912547e-11
A.1.NmC2 0 689 -0.122324 -26.293186 330.586371 1.456478e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 689 11.025436 None None None * * *



Target sequence

, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T,
376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T,
934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G,
1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T,
1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1915_C|A,
1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1963_C|T, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2863_A|G, 2878_A|G, 2881_C|T,
2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC,
3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3790_C|G, 3793_A|G, 3802_T|C,
3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T,
4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 5164_T|C, 5182_G|A, 5194_C|T,
5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A,
5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G,
5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T,
6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C,
6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T,
6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C,
7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G,
7297_A|G, 7306_C|T, 7312_C|T, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C,
7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C,
7721_A|C, 7726_C|A, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G,
8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A,
8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA,
8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T,
8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_G|C, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T,
9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9946_T|C, 9955_A|G, 9970_A|G,
9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): OP508621.1


Target: 835 samples Number of changes: 737
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 150-151, 422-423 BC BR coord: 1605 - 1606, 6596 - 6597
Direction L1: << Initial region span: 1-150,151-185,423-737Gap history (edge excluded): 150-423 -> 185-423
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.26e-09
Rec. model vs L1: 2.13e-26 Rec. model vs L2: 2.47e-21
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 150 13.588398 None None None * * *
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 186 5.023180 NaN NaN NaN * * *
A.1.NmC1 0 151 -0.064207 -35.500402 1525.000805 8.465687e-12
A.1.NmC2 0 151 -0.142154 -69.657054 1593.314108 1.242608e-26
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 423 15.40089 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A,
1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C,
1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|T, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T,
2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A,
2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G,
3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A,
4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA,
4411_A|T, 4420_A|G, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C,
5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C,
6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6530_C|T,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_TA|CT, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C,
6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA,
6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T,
6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T,
7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A,
7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G,
7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG,
7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C,
8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G,
8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G,
8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9454_A|G,
9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G,
9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T,
9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A,
10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 3 (A.1): OP508634.1


Target: 835 samples Number of changes: 638
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 312-313, 480-481 BC BR coord: 3097 - 3098, 8022 - 8023
Direction L1: >> Initial region span: 1-312,313-342,481-638Gap history (edge excluded): 312-481 -> 342-481
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.16e-18
Rec. model vs L1: 3.95e-34 Rec. model vs L2: 1.41e-31
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 312 26.84112 NaN NaN NaN * * *
A.1.NmC2 0 239 13.07756 4.907164 1450.185672 4.205367e-16
|||||

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 343 8.118996 NaN NaN NaN * * *
A.1.NmC2 0 313 0.000000 -73.823850 1549.647700 5.629740e-36
A.1.NmC1 0 313 -0.522213 -37.957649 1477.915297 2.120606e-20
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 481 13.559262 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C,
760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A,
886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A,
1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C,
2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2395_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A,
2545_G|A, 2548_C|T, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A,
3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5602_A|T, 5605_C|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T,
6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G,
6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A,
6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T,
6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G,
7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC,
8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8338_C|T,
8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T,
8458_C|T, 8460_AA|GG, 8463_A|C, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8519_T|C, 8524_C|T, 8526_A|G, 8536_C|T, 8542_G|A, 8545_C|T, 8551_C|T,
8554_C|T, 8560_C|T, 8566_T|C, 8569_C|A, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A,
8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G

Case 3 (A.1): OP508637.1


Target: 835 samples Number of changes: 751
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 558-559, 613-614 BC BR coord: 6985 - 6986, 8742 - 8743
Direction L1: >> Initial region span: 1-388,576-613,614-751Gap history (edge excluded): 388-614 -> 388-576
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.85e-10
Rec. model vs L1: 2.81e-18 Rec. model vs L2: 2.64e-26
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 388 32.746060 NaN NaN NaN * * *
A.1.NmC2 0 43 -0.902677 -33.838172 2419.676344 1.580471e-32
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 576 6.303242 NaN NaN NaN * * *
A.1.NmC1 0 614 -0.199542 -21.385724 550.771447 2.194647e-12
A.1.NmC2 0 614 -0.271001 -36.457725 580.915449 6.228383e-19
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 614 12.271827 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T,
682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A,
1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T,
2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G,
2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2242_T|C, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C,
2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2687_T|C, 2698_C|T,
2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A,
2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G,
3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A,
4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5602_A|T, 5605_C|T, 5614_C|T, 5626_G|T,
5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5992_C|T, 6004_T|C,
6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G,
6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A,
6286_G|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT,
6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A,
6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G,
7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7288_T|G, 7297_A|G, 7306_C|T, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G,
8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A,
9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A,
9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T,
10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A,
10281_A|G, 10297_A|G

Case 3 (A.1): OP508639.1


Target: 835 samples Number of changes: 474
BC: A.1 + A.1.NmC1 BC BR: 316-317 BC BR coord: 8772 - 8773
Direction L1: << Initial region span: 1-316,317-474Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.85e-129
Rec. model vs L1: 1.59e-13Rec. model vs L2: 8.65e-55
Flags: Model_1BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 317 12.761677 NaN NaN NaN * * *
A.1.NmC1 0 50 7.629889 -60.410368 2578.820736 1.669832e-32
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 317 16.949917 NaN NaN NaN * * *
A.1 835 51 3.414556 -14.293089 418.586178 2.694442e-14



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262, 272_.|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G,
367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G,
511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C,
1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C,
1183_T|C, 1207_A|T, 1210_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T,
1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G,
3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C,
4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C,
5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G,
6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A,
6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T,
7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T,
7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A,
9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C,
9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): OP508641.1


Target: 835 samples Number of changes: 697
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 303-304, 463-464 BC BR coord: 4104 - 4105, 7743 - 7744
Direction L1: << Initial region span: 1-303,427-463,464-697Gap history (edge excluded): 303-464 -> 303-427
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.16e-10
Rec. model vs L1: 3.51e-23 Rec. model vs L2: 6.34e-26
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 303 14.664484 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 427 6.171026 NaN NaN NaN * * *
A.1.NmC2 0 460 1.241393 -65.492829 1164.985659 2.321893e-28
A.1.NmC1 0 460 -0.175993 -28.248735 1090.497470 3.476483e-12
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 464 20.476087 None None None * * *



Target sequence

, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T,
376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 432_T|C, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A,
514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A,
691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 1094_T|C, 1096_G|A, 1102_C|A,
1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G,
1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C,
2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA,
2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2545_G|A, 2548_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A,
2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G,
3465_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G,
3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G,
3682_G|T, 3686_T|C, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A,
3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C,
5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A,
5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5752_C|T, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5992_C|T, 5995_A|T, 6004_T|C, 6013_T|C,
6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A,
6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T,
6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T,
6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7108_C|T, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T,
7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA,
8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T,
8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_A|C, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8497_T|A, 8500_G|A, 8505_TGA|CCG,
8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8749_T|C,
8755_G|A, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): OP508571.1


Target: 835 samples Number of changes: 1270
BC: A.1.NmC2 + A.1.NmC1 BC BR: 1235-1236 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-1102,1238-1270Gap history (edge excluded): 1102-1238
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.38e-183Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1102 153.610903 NaN NaN NaN * * *
A.1.NmC1 0 7 0.624153 -422.269352 3750.538705 4.817025e-231
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 1238 2.859189 None None None * * *



Target sequence

, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 283_T|C, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 625_C|T, 628_T|C,
649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C,
784_G|A, 799_A|G, 802_A|G, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G,
931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C,
1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T,
1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T,
1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G,
1572_C|A, 1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|T, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|C,
1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_AT|GC, 1841_T|C, 1843_G|C, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2077_C|T, 2080_A|T, 2083_T|C,
2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A,
2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2540_A|G, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2683_C|T, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A,
2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T,
2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G,
3274_A|G, 3280_G|A, 3283_A|G, 3298_G|T, 3302_A|G, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G,
3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T,
3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3844_G|A, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C,
3895_T|G, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4090_G|A, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C,
4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4270_T|C, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A,
4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4505_C|A, 4519_T|A,
4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|C, 4591_T|C, 4600_T|A, 4603_T|C, 4606_G|A, 4612_C|T, 4618_A|G,
4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4667_T|C, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C,
4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T,
4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C,
4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A,
5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A,
5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5449_T|C, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5605_C|T, 5614_C|T,
5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5719_T|C, 5737_C|G, 5740_G|A, 5760_GA|AG, 5773_G|A, 5776_A|T, 5779_G|A,
5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5941_T|C,
5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5986_T|C, 5989_A|G, 5992_C|T, 6004_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G,
6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A,
6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG,
6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6523_T|C,
6527_T|C, 6530_C|T, 6532_C|G, 6541_G|A, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6946_T|C, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7732_T|C, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7873_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G,
7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T,
8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A,
8602_A|C, 8605_T|C, 8608_T|G, 8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8714_G|C, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A,
8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8848_C|T, 8851_A|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8954_A|C,
8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G,
9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9484_C|G, 9491_G|A, 9499_G|C, 9520_G|C, 9522_T|C,
9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A,
9637_C|T, 9646_G|C, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|A, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10116_A|G,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): OP508653.1


Target: 835 samples Number of changes: 652
BC: A.1.NmC1 + A.1.NmC2 + A.1.NmC1BC BR: 36-37, 83-84 BC BR coord: 450 - 451, 825 - 826
Direction L1: << Initial region span: 1-36,37-83,535-652Gap history (edge excluded): 36-535 -> 83-535
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.82e-03
Rec. model vs L1: 3.51e-08 Rec. model vs L2: 2.22e-246
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 36 5.157331 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 83 5.391301 NaN NaN NaN * * *
A.1 835 147 4.930151 -3.593912 103.187823 0.000141 *
A.1.NmC1 0 83 -4.910617 -5.058400 106.116801 0.000032 * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 535 13.425251 None None None * * *



Target sequence

, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 432_T|C, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1887_T|C, 1915_C|A,
1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C,
3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|T, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G,
3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G,
3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C,
4087_T|C, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T,
4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C,
4453_A|G, 4465, 4466_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A,
5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G,
5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 6430_A|G, 6439_G|A, 6442_A|G,
6445_T|C, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A,
6569_C|T, 6571_A|G, 6586_G|A, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T,
7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C,
7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7580_C|T, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC,
8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G,
8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C,
8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C,
9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G,
10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G,
10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A

Case 3 (A.1): OP508655.1


Target: 835 samples Number of changes: 809
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 55-56, 143-144 BC BR coord: 648 - 649, 2808 - 2809
Direction L1: << Initial region span: 1-55,56-143,144-809Gap history (edge excluded): 55-144 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.05e-07
Rec. model vs L1: 1.61e-10 Rec. model vs L2: 1.01e-31
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 55 7.101716 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 56 5.818563 NaN NaN NaN * * *
A.1.NmC1 0 144 -0.082541 -11.247606 640.495212 3.860052e-08
A.1.NmC2 0 144 -0.168347 -24.035196 666.070393 1.081778e-13
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 144 36.34583 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T,
517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1887_T|C,
1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A,
2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A,
2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G,
3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3480_G|A, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G,
3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T,
3748_T|C, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G,
3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G,
4111_T|C, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G,
4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T,
5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T,
5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C,
5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC,
6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_AC|GT, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G,
6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G,
7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA,
7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A,
7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A,
8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155,
8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG,
9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C,
9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T,
10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G,
10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): OP508701.1


Target: 835 samples Number of changes: 868
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 451-452, 514-515 BC BR coord: 5193 - 5194, 7383 - 7384
Direction L1: << Initial region span: 1-378,452-514,515-868Gap history (edge excluded): 378-515 -> 378-452
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.62e-19
Rec. model vs L1: 4.30e-30 Rec. model vs L2: 3.24e-25
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 378 18.684217 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 452 7.620593 NaN NaN NaN * * *
A.1.NmC1 0 515 -0.099094 -40.644275 673.288550 1.093394e-21
A.1.NmC2 0 515 -0.157902 -47.491893 686.983785 1.164209e-24
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 515 24.564632 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G,
1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A,
1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A,
1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A,
2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|T, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A,
3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C,
3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C,
4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T,
4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A,
4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4397_C|T, 4399_C|T,
4408_GG|AA, 4411_A|T, 4420_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A,
4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C,
4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T,
5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A,
6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G,
7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C,
7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366,
7369_.|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C,
7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T,
8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T,
8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G,
8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C,
8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G,
9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G

Case 3 (A.1): OP508707.1


Target: 835 samples Number of changes: 936
BC: A.1.NmC1 + A.1.NmC1 BC BR: 589-590 BC BR coord: 5640 - 5641
Direction L1: >> Initial region span: 1-468,739-936Gap history (edge excluded): 468-739
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.20e-14
Rec. model vs L1: 2.72e+00Rec. model vs L2: 2.72e+00
Flags: Model_1BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 468 33.441059 NaN NaN NaN * * *
A.1.NmC2 0 416 27.959289 12.700759 1572.598482 3.457967e-08
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 739 22.008976 None None None * * *



Target sequence

, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C,
718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A,
854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A,
991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C,
1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C,
1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A,
1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C,
1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A,
1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G,
1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C,
1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T,
2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2809_T|C, 2812_G|A,
2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T,
2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A,
3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T,
3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G,
3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A,
3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G,
3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C,
3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G,
3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G,
3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C,
4087_T|C, 4089_T|A, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T,
4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G,
4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4769_T|C, 4772_A|G,
4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4949_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C,
4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5113_C|A, 5116_A|G,
5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T,
5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C,
5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T,
7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527,
7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C,
7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G,
8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A,
9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T,
9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9865_G|A,
9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T

Case 3 (A.1): OP508697.1


Target: 835 samples Number of changes: 796
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 446-447, 596-597 BC BR coord: 5442 - 5443, 8742 - 8743
Direction L1: << Initial region span: 1-332,447-596,597-796Gap history (edge excluded): 332-597 -> 332-447
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.57e-23
Rec. model vs L1: 2.56e-35 Rec. model vs L2: 1.03e-22
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 332 13.905693 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 447 6.935148 NaN NaN NaN * * *
A.1.NmC2 0 455 4.219374 -47.676947 1011.353894 1.919457e-24
A.1.NmC1 0 597 -0.199542 -47.999214 1011.998428 1.386860e-24
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 597 21.986268 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C,
1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T,
1855_G|A, 1861_C|T, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1888_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G,
3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A,
3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C,
3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G,
3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A,
3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C,
3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C,
3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T,
4810_C|T, 4816_T|C, 4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|T, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C,
4921_G|A, 4927_A|G, 4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A,
5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T,
5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T,
5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T,
5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366, 7369_.|G,
7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A,
7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A,
7918_A|G, 7920_AG|GA, 7938_AA|GG, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G,
8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C,
8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A,
8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG,
8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G,
9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G,
9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T,
9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA,
9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9796_A|G, 9799_GC|AT, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T,
9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9877_A|G, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C,
10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G,
10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): OP508672.1


Target: 835 samples Number of changes: 890
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 83-84, 146-147 BC BR coord: 822 - 823, 2808 - 2809
Direction L1: << Initial region span: 1-83,84-146,147-890Gap history (edge excluded): 83-147 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.49e-10
Rec. model vs L1: 5.33e-13 Rec. model vs L2: 7.33e-47
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 83 12.454574 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 84 8.354183 NaN NaN NaN * * *
A.1.NmC1 0 147 -0.082541 -14.417840 600.835679 1.285118e-10
A.1.NmC2 0 147 -0.168347 -27.601782 627.203564 2.426286e-16
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 147 49.66869 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 225_AC|GT, 247_T|C, 250_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A,
802_A|G, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A,
1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1887_T|C, 1915_C|A,
1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A,
2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G,
3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C,
3523_TG|AA, 3529_T|C, 3535_T|G, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C,
3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C,
4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4105_C|G, 4111_T|C, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA,
4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A,
4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 5017_G|A, 5020_T|A,
5029_C|T, 5038_C|A, 5047_C|T, 5055_A|C, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G,
5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C,
5284_G|A, 5287_T|C, 5290_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A,
5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 6174_A|G,
6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A,
6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C,
6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6703_C|T, 6706_C|T,
6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T,
6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C,
6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8111_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T,
8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C,
8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8773_C|T, 8782_G|A,
8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG,
8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G,
9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G,
9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T,
9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA,
9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T,
9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9778_C|T, 9787_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G,
9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): OP508674.1


Target: 835 samples Number of changes: 692
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 364-365, 393-394 BC BR coord: 4119 - 4120, 6939 - 6940
Direction L1: >> Initial region span: 1-234,365-393,394-692Gap history (edge excluded): 234-394 -> 234-365
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.54e-22
Rec. model vs L1: 2.39e-36 Rec. model vs L2: 5.57e-24
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 234 22.666504 NaN NaN NaN * * *
A.1.NmC2 0 207 6.084243 -0.565832 2043.131664 1.638492e-15
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 365 11.641308 NaN NaN NaN * * *
A.1.NmC2 0 394 -0.012086 -67.754673 951.509346 3.305138e-35
A.1.NmC1 0 394 -0.237150 -41.506755 899.013510 8.306532e-24
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 394 11.685784 None None None * * *



Target sequence

, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G,
370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T,
517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A,
691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G,
835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A,
970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T,
1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A,
1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G,
1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG,
1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C,
1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T,
2080_A|T, 2083_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A,
3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C,
4105_C|G, 4111_T|C, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C,
6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6526_GT|TC, 6529_CC|TT, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6586_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C,
6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A,
7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T,
7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T, 7600_C|T, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C,
7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A,
9217_T|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9564_T|C, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G,
9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9946_T|C, 9955_A|G, 9970_A|G,
10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): OP508673.1


Target: 835 samples Number of changes: 624
BC: A.1.NmC1 + A.1 + A.1.NmC1BC BR: 55-56, 554-555 BC BR coord: 708 - 709, 9636 - 9637
Direction L1: << Initial region span: 1-55,391-554,555-624Gap history (edge excluded): 55-555 -> 55-391
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.11e-18
Rec. model vs L1: 2.46e-41 Rec. model vs L2: 3.86e-12
Flags: Model_2BP_Best

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 55 6.742519 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 391 8.878924 NaN NaN NaN * * *
A.1.NmC1 0 555 -0.115419 -50.268860 2644.537720 7.457998e-21
A.1.NmC2 0 555 -0.125056 -82.588572 2709.177144 6.858428e-35
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 555 7.975507 NaN NaN NaN * * *
A.1 835 391 1.126428 -13.332573 340.665146 6.544377e-13



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 195_A|G, 327_A|G, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A,
442_G|A, 448_CC|TT, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 535_C|T, 538_C|T, 547_A|C, 553_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G,
595_G|A, 604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T,
1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1224_A|G, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G,
1503_AA|GG, 1507_T|C, 1516_A|G, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1603_C|T, 1606_G|A, 1610_T|C, 1618_G|A,
1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C,
2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G,
3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A,
3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C,
3745_C|T, 3748_T|C, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3919_T|C, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4210_A|T, 4219_A|C,
4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4341_A|G, 4351_T|G, 4360_A|T,
4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C,
4834_A|T, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G,
4930_G|T, 4932_G|A, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4966_C|T, 4969_T|C, 4972_G|A, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T,
5038_C|A, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A, 5350_A|G, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5386_C|T, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C,
5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5479_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C,
7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7231_C|T, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G,
7297_A|G, 7306_C|T, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G,
7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8047_AG|GA, 8050_G|A, 8053_A|G, 8059_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|T, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8386_A|G, 8392_C|T, 8395_G|T, 8398_G|A,
8401_T|C, 8404_C|T, 8422_G|A, 8743_G|A, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T,
8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9772_C|T, 9778_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9982_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T,
10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10104_C|T, 10111_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G

Case 3 (A.1): OP508579.1


Target: 835 samples Number of changes: 997
BC: A.1.NmC2 + A.1.NmC1 BC BR: 960-961 BC BR coord: 9777 - 9778
Direction L1: >> Initial region span: 1-564,968-997Gap history (edge excluded): 564-968
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.51e-186Rec. model vs L2: 1.29e-258
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 564 82.180073 NaN NaN NaN * * *
A.1.NmC1 0 7 0.624153 -299.309362 3384.618725 3.592273e-162
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 968 2.982593 None None None * * *



Target sequence

, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 283_T|C, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A, 354_C|T,
358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT, 488_T|C,
493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A,
742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 799_A|G, 802_A|G, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G,
982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA,
1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A,
1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C,
1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A,
1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|T, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|C, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_AT|GC, 1841_T|C, 1843_G|C,
1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 2003_A|G, 2008_T|C, 2011_A|G,
2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C,
2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2540_A|G, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G,
2644_G|A, 2683_C|T, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2833_G|A, 2836_G|A, 2863_A|G, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT,
3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G,
3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G,
3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3844_G|A, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3895_T|G, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4090_G|A, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4435_G|A, 4438_G|A, 4441_T|C, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A,
6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C,
6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6541_G|A, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T,
6619_T|C, 6622_A|G, 6625_AC|GT, 6631_A|G, 6634_G|T, 6643_C|T, 6658_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T,
6757_TG|CA, 6766_C|A, 6778_CC|TT, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6841_A|T, 6844_C|T, 6847_C|T, 6869_G|A, 6874_A|T,
6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6946_T|C, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T,
6991_G|A, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C,
7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7459_T|C, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7516_A|G, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|T,
7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C,
7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A,
7869_T|C, 7873_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G,
7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T,
8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A,
8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8605_T|C, 8608_T|G,
8611_T|G, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G, 9463_T|C,
9466_TC|CT, 9472_C|T, 9478_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA,
9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10116_A|G,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A,
10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G

Case 3 (A.1): PQ276811.1


Target: 835 samples Number of changes: 1036
BC: A.1.NmC2 + A.1.NmC1 BC BR: 982-983 BC BR coord: 9798 - 9799
Direction L1: >> Initial region span: 1-537,987-1036Gap history (edge excluded): 537-987
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.84e-177Rec. model vs L2: 9.46e-318
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 537 26.138536 NaN NaN NaN * * *
A.1.NmC1 0 33 2.313329 -472.484551 3778.969102 1.583716e-203
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 987 1.160477 None None None * * *



Target sequence

, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 337_C|T, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 442_G|A, 449_C|T, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 607_A|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A,
655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 802_A|G,
823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C,
943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A,
1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|A, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T,
1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T,
1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1480_A|G, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG,
1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1636_T|C, 1642_G|C,
1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1855_G|A,
1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1909_C|T, 1915_C|A, 1924_T|C, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G,
2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A,
2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2476_T|C, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C,
2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2584_A|G, 2596_C|T, 2599_T|C, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C,
2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|G, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C,
2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C,
3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3187_A|G, 3193_C|T,
3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3289_T|C, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G,
3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G,
3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G,
3556_A|C, 3568_CC|GT, 3571_A|G, 3577_A|G, 3589_A|C, 3595_A|G, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G,
3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3910_G|A, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|A, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4099_C|T, 4103_C|T, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C,
4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A,
6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6325_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A,
6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6490_T|C, 6493_A|G, 6508_AA|GG, 6517_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6544_A|G, 6547_C|T, 6550_T|C,
6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6646_C|T, 6649_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6733_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T,
6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6895_A|G, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A,
6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6961_A|C, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 6994_A|G, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C,
7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7286_C|T, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G,
7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G,
7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7507_C|T, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7571_A|C, 7579_TC|CT, 7597_A|G, 7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G,
7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7738_G|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C,
7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T,
7900_T|C, 7912_T|G, 7915_G|A, 7918_A|G, 7920_AG|GA, 7927_G|T, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G,
8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G,
8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A,
8593_G|A, 8600_G|A, 8602_A|T, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G,
8749_T|C, 8755_G|A, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8821_C|T, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G,
8929_G|A, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|T,
9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9590_A|G,
9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|C, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G,
9754_T|C, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9829_T|C, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T,
9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G,
10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T

Case 3 (A.1): PV710608.1


Target: 835 samples Number of changes: 758
BC: A.1.NmC2 + A.1.NmC1 BC BR: 724-725 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-232,727-758Gap history (edge excluded): 232-727
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.14e-184Rec. model vs L2: 6.11e-273
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 232 26.093483 NaN NaN NaN * * *
A.1 835 430 4.236542 -15.897928 2839.795855 29584.326798 *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 727 3.024741 None None None * * *



Target sequence

, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 625_C|T, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T,
694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T, 781_T|C, 784_G|A, 799_A|G, 802_A|G, 826_A|G, 829_G|A, 832_A|G, 835_C|G,
838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T,
973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G,
1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A,
1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A,
1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G,
1522_G|A, 1525_G|A, 1528_A|G, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T,
1642_G|T, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|C, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A,
1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_AT|GC, 1841_T|C, 1843_G|C,
1852_G|A, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 2003_A|G, 2008_T|C,
2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G,
2125_T|C, 2128_C|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T,
3308_A|G, 3310_CA|TG, 3316_T|C, 3319_C|A, 3321_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C,
3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G,
3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 4006_CG|AA, 4013_T|C, 4016_T|A, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4053_AT|GC,
4056_TC|CA, 4062_A|G, 4066_C|T, 4081_T|C, 4087_T|C, 4090_G|A, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5207_T|C, 5212_C|T, 5215_G|A, 5218_C|T, 5224_G|A, 5230_C|G,
5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5338_C|T, 5344_G|A, 5346_G|A,
5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC,
7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7696_C|T, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7873_C|T, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G,
8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8063_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A,
8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|C, 8167_C|G, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T,
8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T, 8782_G|A,
8788_C|T, 8792_C|T, 8815_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8848_C|T, 8851_A|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8954_A|C, 8956_GAA|ACG, 8965_C|T,
8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G,
9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C,
9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9445_C|T, 9454_A|G,
9463_T|C, 9466_TC|CT, 9472_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA,
9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T,
9703_C|A, 9709_TA|GC, 9715_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T,
9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|A, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9985_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10116_A|G, 10129_G|A, 10132_A|G, 10134_T|C,
10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G,
10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): PP477075.1


Target: 835 samples Number of changes: 1474
BC: A.1 + A.1.NmC2 + A.1 BC BR: 1417-1418, 1438-1439 BC BR coord: 10248 - 10249, 10360 - 10361
Direction L1: >> Initial region span: 1-1417,1418-1437,1445-1474Gap history (edge excluded): 1417-1445 -> 1437-1445
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.71e-24
Rec. model vs L1: 2.61e+02Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1417 191.845915 None None None * * *
|||||

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1437 7.612505 NaN NaN NaN * * *
A.1.NmC1 0 1425 0.777482 -59.983015 163.966030 9.652456e-26
A.1 835 1418 -0.101863 -3.342011 50.684021 3.848121e-01 *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1445 2.25698 None None None * * *



Target sequence

, 80_A|G, 117_AC|TA, 166_A|T, 171_G|A, 178_T|C, 226_C|T, 247_T|C, 262_C|T, 280_CA|TG, 284_T|C, 294_AA|GG, 301_C|T, 304_A|T, 307_C|T, 310_CC|TT, 313_A|G, 318_G|A, 320_T|C, 322_G|A, 327_A|G,
346_A|G, 349_CT|GC, 352_G|A, 354_C|T, 361_A|G, 363_G|A, 367_A|G, 385_C|G, 388_TT|CC, 400_A|T, 409_A|G, 421_T|A, 430_T|A, 433_TC|CT, 442_G|T, 448_C|T, 451_A|G, 454_T|C, 467_T|C, 475_G|T,
488_T|C, 496_G|C, 499_A|G, 501_A|G, 514_CC|TT, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 584_T|C, 589_A|G, 596_T|A, 598_C|T, 604_C|T, 607_A|G, 610_C|T, 613_A|C, 628_T|C, 634_T|C,
637_C|T, 649_G|A, 655_A|T, 658_T|C, 664_T|A, 670_C|T, 676_C|T, 682_G|A, 691_C|T, 697_A|G, 700_C|T, 703_A|T, 709_T|C, 718_C|T, 724_725, 727_728, 732_736, 747_.|GTCTAGAAG, 757_C|T, 760_G|A,
763_T|C, 766_G|A, 790_C|T, 799_A|G, 823_T|C, 826_A|G, 829_G|A, 833_C|T, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|A, 877_A|G, 883_G|A, 886_TC|CT, 890_A|G, 898_C|T, 902_C|T, 904_T|G,
910_A|G, 931_C|T, 940_CC|TT, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 967_C|T, 973_A|G, 985_T|A, 991_T|A, 997_C|T, 1036_T|C, 1042_T|C, 1045_CC|TT, 1051_G|A, 1054_A|G, 1066_C|A, 1072_T|G, 1084_C|T,
1090_T|C, 1102_C|A, 1108_A|G, 1111_G|A, 1117_A|T, 1127_A|G, 1138_G|A, 1140_TG|CA, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_T|C, 1174_T|G, 1189_C|T, 1204_T|C, 1207_A|T, 1210_G|A,
1216_C|T, 1219_A|G, 1222_T|C, 1228_G|A, 1231_C|T, 1234_A|G, 1237_G|A, 1240_CA|TC, 1243_T|C, 1246_G|C, 1249_C|T, 1252_G|A, 1255_C|A, 1261_T|C, 1270_A|G, 1279_C|G, 1282_T|C, 1285_C|T, 1300_G|A,
1306_G|A, 1321_C|T, 1333_T|C, 1339_C|T, 1342_A|G, 1351_TT|CC, 1366_T|C, 1378_T|C, 1390_C|T, 1393_A|G, 1399_AT|GC, 1408_A|T, 1411_G|A, 1423_A|G, 1433_A|G, 1435_C|T, 1438_C|T, 1441_T|C,
1453_G|A, 1471_C|T, 1474_C|T, 1480_A|G, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1504_A|G, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1534_G|A, 1544_G|A, 1546_T|C, 1552_T|C,
1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1603_C|T, 1606_G|A, 1609_C|T, 1618_G|A, 1621_A|T, 1639_C|T, 1642_G|T, 1660_T|C, 1669_C|G, 1675_T|C, 1678_A|G, 1684_G|A, 1690_C|T,
1693_C|A, 1701_G|A, 1705_A|G, 1723_G|A, 1732_CT|TC, 1738_A|G, 1747_T|C, 1753_C|T, 1760_A|C, 1765_T|C, 1782_A|G, 1785_A|G, 1792_T|G, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_T|C,
1819_T|A, 1822_C|T, 1855_G|A, 1858_A|G, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1879_C|T, 1887_T|C, 1900_C|T, 1912_T|C, 1915_C|A, 1921_C|T, 1926_TT|CC, 1946_T|C, 1960_C|T, 1969_T|C, 1978_A|G,
1993_T|C, 2000_G|T, 2003_A|G, 2008_T|C, 2020_G|A, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|G, 2038_C|A, 2044_A|C, 2053_T|G, 2059_A|G, 2063_C|T, 2080_A|C, 2083_T|C, 2089_A|G, 2098_C|T, 2101_T|C,
2104_C|A, 2112_GA|CG, 2116_A|G, 2119_T|C, 2122_A|T, 2128_C|G, 2131_T|C, 2146_A|G, 2152_A|C, 2164_A|G, 2188_A|G, 2193_TG|CA, 2201_C|T, 2209_C|T, 2215_A|G, 2218_CA|TG, 2221_C|T, 2224_C|T,
2230_T|C, 2239_C|T, 2248_G|A, 2251_C|T, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2275_T|A, 2278_T|C, 2280_C|T, 2290_C|T, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_AC|GT, 2350_G|A, 2353_A|C,
2376_CA|TG, 2395_C|T, 2408_T|C, 2413_A|T, 2419_G|C, 2432_T|C, 2437_T|C, 2446_T|G, 2455_T|C, 2464_C|T, 2470_C|T, 2488_G|A, 2494_G|A, 2497_C|T, 2500_A|G, 2503_T|C, 2506_T|A, 2515_A|C, 2518_T|C,
2521_A|G, 2524_C|T, 2527_T|A, 2533_C|T, 2548_C|T, 2566_T|C, 2569_T|G, 2575_G|A, 2581_A|T, 2593_A|G, 2599_T|C, 2602_T|C, 2605_A|G, 2620_CC|TT, 2626_T|C, 2635_C|T, 2641_T|G, 2644_G|A, 2650_G|A,
2659_A|G, 2668_A|G, 2686_T|C, 2695_A|G, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_T|C, 2731_A|C, 2734_G|A, 2737_TG|CA, 2740_T|C, 2743_C|T, 2752_A|G, 2755_T|A,
2761_A|T, 2776_G|T, 2782_TC|CT, 2788_G|A, 2794_T|C, 2803_T|C, 2811_A|G, 2815_C|T, 2824_C|T, 2827_C|T, 2833_G|A, 2836_G|A, 2860_T|C, 2863_A|G, 2878_A|G, 2887_T|C, 2894_C|A, 2896_G|A, 2899_C|G,
2908_T|C, 2920_G|A, 2947_A|G, 2950_C|A, 2962_C|T, 2983_A|G, 2986_C|T, 3007_T|G, 3010_A|G, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3064_T|C, 3070_A|G, 3073_A|G,
3079_G|A, 3091_C|A, 3098_T|C, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3160_T|G, 3169_T|C, 3172_A|C, 3187_A|G, 3193_C|T, 3205_T|G, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|A, 3238_T|C, 3244_G|A, 3247_C|T, 3250_A|G, 3271_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|TGG, 3334_G|T, 3337_A|G, 3343_A|T,
3349_A|G, 3358_G|C, 3361_T|C, 3364_C|T, 3370_AG|GA, 3382_A|G, 3394_C|A, 3397_C|A, 3400_C|T, 3412_T|A, 3421_C|T, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3457_T|C, 3460_G|A, 3469_A|G, 3472_G|A,
3478_A|C, 3484_T|C, 3490_G|T, 3493_C|T, 3496_C|A, 3502_T|G, 3511_A|G, 3514_AA|GG, 3517_A|C, 3523_T|A, 3529_T|C, 3535_TT|GC, 3562_A|G, 3566_G|T, 3569_C|T, 3571_A|G, 3573_G|A, 3576_AA|GG,
3589_A|C, 3598_G|A, 3601_G|A, 3610_AG|CA, 3620_T|C, 3628_A|C, 3632_C|T, 3637_C|T, 3640_G|A, 3643_A|G, 3649_T|C, 3652_CC|GT, 3655_T|G, 3658_T|C, 3667_A|G, 3670_CACA|TGTG, 3679_T|G, 3682_G|T,
3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3727_T|C, 3733_G|C, 3739_T|C, 3745_C|T, 3751_A|G, 3757_A|G, 3760_A|G, 3763_G|A, 3772_C|T, 3784_C|T, 3790_C|A, 3793_A|G, 3820_G|A, 3826_A|G,
3832_A|T, 3847_T|A, 3860_G|A, 3868_C|A, 3871_C|G, 3883_T|C, 3886_A|T, 3895_T|G, 3898_T|C, 3901_C|T, 3908_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3937_A|G, 3940_A|G, 3946_TA|CG, 3959_C|T, 3961_C|G,
3967_T|G, 3973_G|A, 3982_C|G, 3985_T|A, 4001_C|A, 4006_CG|AA, 4009_A|G, 4013_T|C, 4021_TG|CA, 4030_T|C, 4054_T|C, 4056_TC|CA, 4063_C|T, 4066_C|T, 4075_G|A, 4081_T|C, 4087_T|C, 4102_A|G,
4105_C|G, 4108_A|C, 4120_C|A, 4138_G|A, 4142_C|T, 4147_T|C, 4150_A|C, 4154_C|A, 4165_C|A, 4171_T|C, 4174_G|A, 4183_T|C, 4186_C|T, 4198_G|A, 4204_C|T, 4210_A|G, 4219_A|C, 4225_A|G, 4229_C|T,
4234_A|G, 4246_T|C, 4258_G|A, 4264_C|T, 4267_T|G, 4270_T|C, 4274_A|G, 4285_A|G, 4289_C|A, 4291_C|T, 4304_G|A, 4306_T|C, 4313_G|A, 4321_G|A, 4330_G|A, 4333_A|C, 4336_G|A, 4341_A|G, 4348_T|A,
4351_T|A, 4360_A|T, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4411_A|T, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4456_G|T, 4465_C|T, 4469_G|A, 4474_G|C, 4483_G|A,
4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CA, 4531_C|T, 4540_G|T, 4544_C|T, 4547_T|C, 4549_T|C, 4557_G|A, 4576_G|A, 4579_T|C, 4583_T|C, 4585_G|C, 4594_T|C, 4598_A|G,
4600_T|A, 4605_AG|CA, 4609_CA|TG, 4612_C|T, 4618_A|G, 4628_C|T, 4630_G|A, 4639_G|A, 4651_A|T, 4654_C|T, 4666_CT|TC, 4672_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4693_A|G, 4696_G|A, 4711_G|C,
4720_A|G, 4732_C|G, 4741_A|C, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4765_G|A, 4769_T|C, 4771_GA|AG, 4774_T|C, 4778_T|A, 4780_T|C, 4792_A|C, 4813_T|C, 4819_C|T, 4829_T|C, 4834_A|G,
4840_A|G, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|T, 4873_G|A, 4876_T|C, 4878_TT|CC, 4882_A|C, 4900_C|T, 4903_C|T, 4912_A|G, 4915_G|A, 4919_T|C, 4924_C|T, 4927_A|G, 4930_G|T, 4939_G|C, 4948_C|T,
4954_T|G, 4957_C|G, 4969_T|C, 4978_C|T, 4981_T|C, 4984_A|C, 4987_A|C, 4993_T|C, 5008_C|T, 5011_A|T, 5020_T|A, 5024_C|T, 5026_G|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T,
5068_C|T, 5080_G|A, 5088_TG|CA, 5092_G|A, 5098_A|G, 5101_A|G, 5103_A|G, 5107_G|A, 5113_C|T, 5116_A|G, 5119_G|A, 5140_A|G, 5152_TG|AA, 5155_C|T, 5161_T|C, 5164_T|C, 5173_A|T, 5176_T|C,
5179_G|A, 5182_G|A, 5185_A|T, 5188_A|G, 5191_T|C, 5194_C|T, 5200_A|C, 5207_T|C, 5212_C|T, 5215_G|A, 5218_C|T, 5230_CT|GC, 5239_T|G, 5245_GT|TC, 5251_C|T, 5254_C|T, 5257_C|T, 5269_T|C,
5272_T|C, 5275_A|G, 5287_T|C, 5293_C|T, 5299_G|A, 5302_C|T, 5305_G|A, 5308_A|G, 5323_T|C, 5326_T|C, 5332_T|G, 5344_G|A, 5346_GA|AG, 5368_C|T, 5380_A|G, 5383_T|A, 5393_T|C, 5398_A|G, 5404_T|C,
5407_G|A, 5410_T|G, 5413_T|G, 5416_C|T, 5422_A|G, 5428_C|T, 5431_T|C, 5440_A|G, 5452_G|A, 5458_A|G, 5461_T|C, 5464_C|T, 5470_C|A, 5473_T|C, 5479_T|C, 5488_G|A, 5491_C|T, 5500_G|A, 5530_A|T,
5539_G|T, 5542_T|A, 5545_G|A, 5569_A|G, 5575_T|G, 5584_A|G, 5593_A|G, 5596_G|A, 5599_C|T, 5602_A|T, 5605_C|T, 5623_A|G, 5626_G|T, 5632_C|T, 5641_A|G, 5644_T|C, 5662_A|C, 5668_C|T, 5683_A|G,
5689_A|G, 5692_T|C, 5701_T|A, 5708_T|C, 5710_G|A, 5713_T|C, 5716_G|A, 5722_A|G, 5737_C|G, 5740_G|A, 5749_A|G, 5758_G|A, 5760_G|A, 5764_A|G, 5773_G|A, 5776_A|C, 5779_G|A, 5797_T|C, 5800_A|C,
5833_C|T, 5836_T|C, 5839_C|T, 5846_C|A, 5872_T|C, 5875_G|A, 5893_A|G, 5914_A|G, 5917_G|A, 5926_T|G, 5929_C|T, 5932_C|A, 5935_A|T, 5938_C|T, 5941_T|C, 5947_T|C, 5953_G|A, 5956_G|A, 5968_G|A,
5971_A|G, 5974_T|C, 5977_C|A, 5980_C|T, 5983_A|G, 5989_A|G, 5992_C|T, 5998_C|T, 6001_C|T, 6004_T|C, 6023_A|G, 6025_T|C, 6034_C|T, 6037_C|T, 6047_T|C, 6052_G|A, 6065_T|C, 6067_G|A, 6106_C|T,
6113_G|A, 6115_T|A, 6118_A|G, 6121_A|G, 6124_T|A, 6127_A|G, 6136_T|C, 6142_T|A, 6145_T|C, 6154_AC|GT, 6157_G|A, 6160_G|A, 6169_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6199_T|C, 6220_T|C, 6223_G|A,
6229_A|G, 6244_TT|AC, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6280_C|T, 6283_T|G, 6292_T|C, 6307_C|T, 6310_C|T, 6316_A|G, 6322_G|A, 6334_T|C, 6340_A|G, 6346_A|G, 6351_A|G, 6361_C|G, 6364_A|C,
6367_G|A, 6373_T|C, 6379_A|G, 6385_G|T, 6403_G|T, 6406_GT|TG, 6409_T|C, 6415_T|C, 6418_T|A, 6427_T|C, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6445_T|G, 6448_T|A, 6451_A|G, 6457_A|G, 6478_T|A,
6490_T|C, 6493_A|G, 6508_A|G, 6514_T|C, 6517_C|T, 6523_T|C, 6529_CC|TT, 6532_CC|GA, 6547_C|T, 6550_T|C, 6569_C|T, 6571_A|G, 6595_A|G, 6611_A|G, 6613_AC|TT, 6622_AC|GT, 6625_A|G, 6631_A|G,
6634_G|T, 6664_A|G, 6667_C|A, 6673_T|C, 6682_T|C, 6688_G|A, 6703_C|T, 6706_C|T, 6709_T|C, 6715_T|C, 6724_C|T, 6730_A|G, 6733_C|T, 6745_T|C, 6757_TG|CA, 6766_C|G, 6772_C|T, 6779_C|T, 6790_T|G,
6794_A|G, 6796_C|T, 6799_C|A, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6859_C|T, 6866_C|T, 6874_A|C, 6876_C|T, 6883_A|G, 6889_C|T, 6892_G|A,
6895_A|G, 6898_C|T, 6902_C|T, 6907_G|A, 6910_A|G, 6916_A|G, 6919_G|A, 6934_G|A, 6943_A|G, 6955_T|C, 6959_T|G, 6969_GT|AC, 6976_G|A, 6979_T|C, 6986_C|T, 6988_G|A, 7003_C|T, 7009_A|T, 7012_G|C,
7015_C|T, 7027_T|G, 7030_A|G, 7039_T|C, 7046_T|C, 7054_C|T, 7066_C|T, 7069_A|G, 7079_C|T, 7081_G|A, 7084_T|C, 7096_AG|TA, 7105_A|G, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C,
7141_A|G, 7156_T|C, 7171_G|C, 7174_G|A, 7177_GG|AA, 7180_C|T, 7211_C|T, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7243_C|T, 7247_T|A, 7249_T|C, 7255_T|C, 7258_A|G, 7261_T|C, 7279_G|A, 7286_C|T,
7288_T|G, 7297_A|G, 7300_G|A, 7306_C|T, 7312_C|T, 7318_CG|TA, 7321_G|A, 7324_C|T, 7327_T|A, 7339_G|A, 7366_T|C, 7369_T|G, 7384_T|C, 7396_A|G, 7402_T|A, 7405_A|G, 7412_C|T, 7414_T|A, 7420_T|C,
7423_C|T, 7426_C|T, 7429_A|G, 7432_T|C, 7438_T|A, 7450_A|G, 7453_G|C, 7456_C|T, 7465_G|A, 7468_T|C, 7480_CC|AT, 7483_A|G, 7492_T|A, 7495_CT|TC, 7498_A|G, 7501_G|A, 7504_G|A, 7516_A|G,
7519_C|T, 7528_T|C, 7531_T|G, 7552_C|G, 7561_A|G, 7571_A|C, 7580_C|T, 7582_C|T, 7597_A|T, 7612_A|C, 7630_A|G, 7634_C|A, 7642_C|A, 7645_G|A, 7651_A|G, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C,
7691_T|C, 7701_GA|AG, 7712_T|C, 7717_T|C, 7726_C|A, 7732_T|C, 7735_G|A, 7744_T|C, 7750_T|A, 7753_G|A, 7762_G|A, 7765_T|C, 7771_C|T, 7789_C|T, 7798_G|T, 7804_C|G, 7807_G|A, 7813_C|T, 7816_A|T,
7819_G|A, 7822_A|G, 7825_G|A, 7831_C|T, 7837_G|A, 7855_G|A, 7861_T|C, 7869_T|C, 7876_G|A, 7879_G|A, 7882_T|C, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7906_C|T, 7915_G|A, 7918_A|G, 7921_G|A,
7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7969_G|A, 7990_T|C, 8011_C|T, 8014_C|T, 8023_A|G, 8029_T|C, 8041_A|G, 8044_A|G, 8053_A|G, 8065_T|C, 8071_T|C, 8074_C|T, 8086_A|G,
8089_AT|TC, 8092_G|A, 8095_A|G, 8098_G|A, 8101_C|G, 8104_A|C, 8120_G|A, 8123_A|C, 8134_T|C, 8137_T|C, 8140_A|T, 8143_A|G, 8152_G|T, 8154_C|G, 8158_T|C, 8161_G|T, 8167_C|G, 8169_A|G, 8173_C|T,
8188_A|G, 8209_T|G, 8212_C|A, 8215_G|A, 8218_A|G, 8224_AT|GA, 8245_C|T, 8248_A|G, 8251_A|G, 8254_G|C, 8260_G|A, 8266_T|C, 8269_C|T, 8275_G|A, 8281_C|T, 8284_T|C, 8290_A|G, 8296_C|T, 8299_C|T,
8308_A|G, 8317_C|T, 8320_TG|CA, 8329_T|C, 8341_A|G, 8344_A|G, 8354_C|T, 8356_G|A, 8362_G|A, 8380_T|A, 8383_A|C, 8398_G|A, 8408_A|G, 8422_G|A, 8425_A|G, 8434_T|G, 8437_G|A, 8440_A|G, 8446_G|A,
8449_A|G, 8452_C|A, 8460_AA|GG, 8463_AG|CA, 8470_A|C, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CAG, 8510_T|A, 8512_T|C, 8518_T|C, 8527_T|C, 8545_C|T, 8551_C|T, 8557_T|C, 8574_A|G,
8584_A|G, 8587_T|C, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|C, 8608_T|A, 8611_T|G, 8614_T|C, 8617_A|G, 8629_T|C, 8632_A|C, 8638_C|T, 8650_G|A, 8656_A|T, 8671_T|A, 8680_C|T, 8683_T|C, 8692_G|A,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8770_C|T, 8773_C|T, 8782_G|A, 8800_A|G, 8808_A|G, 8815_A|G, 8824_A|G, 8830_A|G, 8833_A|G, 8837_A|G, 8839_T|G, 8851_A|C, 8854_T|C,
8866_T|C, 8872_T|C, 8874_A|T, 8902_T|C, 8923_C|T, 8926_A|G, 8929_G|A, 8939_C|T, 8954_A|C, 8957_AA|CG, 8962_G|A, 8968_A|G, 8971_A|G, 8974_C|T, 9019_G|A, 9022_G|A, 9040_A|G, 9043_A|G, 9046_G|A,
9052_C|T, 9055_T|C, 9061_A|C, 9067_T|C, 9074_C|T, 9082_G|C, 9085_G|A, 9100_G|A, 9115_G|A, 9133_T|A, 9142_A|G, 9151_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9175_A|G, 9179_T|C, 9182_C|T,
9187_A|C, 9190_T|C, 9212_A|C, 9214_G|A, 9217_T|A, 9235_G|A, 9244_C|A, 9259_G|A, 9274_A|G, 9277_C|T, 9280_T|G, 9283_T|C, 9299_T|C, 9313_C|T, 9319_T|C, 9322_C|T, 9324_A|G, 9328_A|G,
9335_CAA|TTG, 9343_G|A, 9361_G|A, 9367_A|G, 9379_G|C, 9382_G|A, 9391_C|G, 9397_A|T, 9406_C|A, 9427_A|G, 9430_A|G, 9439_A|G, 9445_C|T, 9467_C|T, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C,
9527_A|G, 9529_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CG, 9562_A|G, 9565_T|C, 9571_C|A, 9573_GG|AA, 9577_G|T, 9590_A|G, 9598_C|T, 9601_A|C, 9610_AC|GT,
9625_G|A, 9637_C|T, 9646_G|C, 9652_G|C, 9658_C|T, 9670_C|T, 9679_C|T, 9685_C|T, 9691_C|T, 9706_G|A, 9709_TA|GC, 9712_A|C, 9733_G|A, 9745_G|A, 9754_T|C, 9766_G|A, 9769_C|G, 9775_T|C, 9790_T|C,
9796_A|G, 9802_G|A, 9817_G|A, 9820_T|C, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_C|A, 9859_A|G, 9865_G|A, 9868_G|T, 9871_T|C, 9880_C|T, 9898_A|G, 9901_A|G, 9904_T|A, 9910_C|A, 9919_C|T,
9938_C|T, 9946_T|C, 9955_A|G, 9970_A|G, 9976_AT|TC, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|G, 10018_A|G, 10024_C|T, 10027_A|C, 10030_A|G, 10036_GA|TG, 10051_G|A, 10066_G|A, 10093_A|G,
10096_A|G, 10103_AC|GT, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA, 10159_T|C, 10162_T|C, 10174_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10213_T|C,
10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_TT|CC, 10243_A|G, 10246_C|G, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10294_C|T, 10297_A|G,
10309_C|T, 10312_G|A, 10315_T|C, 10331_C|T, 10336_A|G, 10338_TG|CC, 10342_T|C, 10348_T|C, 10351_C|T, 10355_A|G, 10358_A|G, 10363_C|T, 10365_AA|TG, 10369_10377, 10381_10382, 10385,
10391_10397, 10403_10405, 10407, 10409_10411, 10412_C|G, 10416_10417, 10421_10429, 10434_10442, 10444_10445, 10450, 10451_C|T, 10455_10460, 10464_10475, 10522, 10524_G|A, 10533_A|G,
10535_T|G, 10547_A|G, 10554_CAC|TGT, 10558_A|G, 10562_T|C, 10605_A|C, 10607_C|G, 10620_A|T, 10625_C|T, 10635_G|A, 10639_C|T, 10647_C|T, 10653_.|G, 10657_AAG|CCA, 10681_C|T

Case 3 (A.1): PP869888.1


Target: 835 samples Number of changes: 1168
BC: A.1.NmC2 + A.1 BC BR: 567-568 BC BR coord: 4833 - 4834
Direction L1: >> Initial region span: 1-396,1162-1168Gap history (edge excluded): 396-1162
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.35e-189Rec. model vs L2: 2.01e+07
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 396 15.083040 NaN NaN NaN * * *
A.1 835 51 2.397856 -36.205091 1466.410183 2.273206e-14
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1162 0.212625 None None None * * *



Target sequence

, 346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 433_TC|CT, 436_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 529_T|C, 538_C|T, 547_A|C, 556_G|T, 559_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T,
604_C|T, 610_C|T, 613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C,
1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1106_C|T, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G,
1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T,
1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T,
1438_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1552_T|C,
1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A,
1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G,
1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C,
1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A,
2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G,
2193_TG|CA, 2197_A|G, 2215_A|G, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2254_C|T, 2257_T|A, 2260_G|A, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T,
2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C,
2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C,
2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2728_TC|CT, 2734_G|A,
2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G,
3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C,
3172_A|C, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C,
3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A,
3423_AT|GC, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3457_T|C, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_TC|CT, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_TT|GC, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T,
3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C,
3782_C|T, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C,
4153_TC|CA, 4165_CA|AG, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|G, 4273_GA|AG,
4276_T|C, 4288_AC|GA, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_G|A, 4411_A|T,
4420_A|G, 4429_G|A, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4480_C|T, 4483_G|A, 4489_C|T, 4495_T|C, 4498_G|A, 4504_CC|TA, 4519_T|A, 4522_TC|CT, 4525_GC|AT, 4531_C|T, 4540_G|T, 4544_C|T,
4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4669_G|A, 4678_C|T,
4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C,
4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4867_G|A, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4885_A|G, 4888_G|A, 4894_G|A, 4897_C|G, 4900_C|T,
4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|C, 4939_G|A, 4951_G|T, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T,
5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5977_C|T, 5986_T|C, 5989_A|G, 6001_C|T, 6004_T|C,
6013_T|C, 6023_A|G, 6025_T|C, 6031_C|A, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G,
6142_T|A, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6205_C|T, 6211_C|T, 6220_T|C, 6223_G|A, 6235_C|T, 6244_T|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G,
6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6331_G|A, 6334_T|C, 6361_C|T, 6365_A|C, 6373_T|C, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6628_G|A, 6631_A|G,
6634_G|T, 6638_A|G, 6643_C|T, 6658_T|C, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G,
6796_C|T, 6799_C|T, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6869_G|A, 6874_A|T, 6876_CG|TA, 6889_C|T,
6892_G|A, 6902_C|T, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6958_TT|CG, 6964_C|T, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7003_C|T,
7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7075_C|T, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G,
7156_T|C, 7171_G|T, 7174_GC|AT, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7294_G|A, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7341_A|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7527, 7531_.|G, 7552_C|G, 7564_A|G, 7567_C|T, 7571_A|C, 7579_TC|CT, 7597_A|T,
7612_A|C, 7624_A|G, 7634_C|A, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7717_T|C, 7721_A|C, 7726_C|A,
7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A,
7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_A|G, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G,
7987_A|G, 7990_T|C, 7993_G|A, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8048_GT|AC, 8053_A|G, 8059_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G,
8104_A|C, 8107_G|A, 8110_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT,
8221_G|A, 8224_AT|GC, 8245_C|T, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8329_T|C,
8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8449_A|G, 8452_C|A,
8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8536_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T,
8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T,
8692_G|A, 8704_T|C, 8707_A|G, 8737_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8773_C|T, 8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8833_A|G, 8839_T|A, 8911_G|A, 8923_C|T,
8926_A|G, 8939_C|T, 8954_A|C, 8956_GAA|ACG, 8980_T|C, 8983_G|A, 9010_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|T, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G,
9160_G|T, 9166_C|T, 9169_T|C, 9172_C|T, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A,
9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_AA|TG, 9340_A|T, 9343_G|A, 9361_G|A, 9367_A|G, 9379_GT|CC, 9385_A|G, 9388_A|G, 9391_C|T, 9397_A|T, 9403_A|G, 9406_C|T, 9424_TC|CA,
9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9559_AT|CA, 9562_A|T,
9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9616_GA|AC, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9664_C|T, 9670_C|T, 9679_C|T,
9685_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10117_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A,
10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10279_G|A, 10281_A|G, 10287_C|T, 10297_A|G, 10303_C|T, 10315_T|C, 10330_C|T

Case 3 (A.1): PV710607.1


Target: 835 samples Number of changes: 883
BC: A.1.NmC2 + A.1.NmC1 BC BR: 849-850 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-509,852-883Gap history (edge excluded): 509-852
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.14e-184Rec. model vs L2: 3.96e-264
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 509 46.108291 NaN NaN NaN * * *
A.1 835 49 0.396859 -35.987919 2879.975839 1.336384e-29
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 852 3.024741 None None None * * *



Target sequence

, 178_T|C, 192_A|G, 218_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 283_T|C, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G,
1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1132_T|A, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G,
1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A,
1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C,
1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C,
1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1609_CT|TC, 1618_G|A, 1621_A|T, 1642_G|T, 1666_T|C,
1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|C, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A,
1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_AT|GC, 1841_T|C, 1843_G|C, 1852_G|A, 1855_G|A,
1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C,
2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2077_C|T, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A,
2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A,
2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T,
2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T,
2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A,
3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C,
3220_T|C, 3223_C|T, 3226_T|G, 3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3272_G|A, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_C|A, 3321_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T,
3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G,
3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C,
3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C,
3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3844_G|A, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A,
3947_AC|GT, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T,
4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4090_G|A, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C,
4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C,
4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4408_GG|AA, 4411_A|T, 4420_A|G, 4429_G|A,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T,
4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C,
4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7696_C|T, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A,
7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7873_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7924_A|G, 7939_A|G,
7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8063_C|T,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|C, 8167_C|G,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C,
8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C,
8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8443_C|T, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 9485_T|C,
9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9511_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|A, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9985_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G,
10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10116_A|G, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10144_A|G, 10148_A|C, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): PV710587.1


Target: 835 samples Number of changes: 909
BC: A.1.NmC2 + A.1.NmC1 BC BR: 875-876 BC BR coord: 10103 - 10104
Direction L1: >> Initial region span: 1-530,878-909Gap history (edge excluded): 530-878
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.16e-184Rec. model vs L2: 1.19e-306
Flags: Model_2BP_Bad_L1_opp

A.1.NmC2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 530 52.430835 None None None * * *
|||||

A.1.NmC1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 878 3.024741 None None None * * *



Target sequence

, 178_T|C, 192_A|G, 218_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 283_T|C, 295_A|G, 301_C|T, 304_A|T, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G, 352_G|A,
354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C, 473_ACG|GTT,
488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 568_C|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C, 625_C|T,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 775_C|T,
781_T|C, 784_G|A, 799_A|G, 802_A|G, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 886_TC|CT, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 982_C|T, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1171_TC|CA, 1174_T|C, 1183_T|C, 1207_A|T, 1217_C|T, 1219_A|G,
1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C,
1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1468_A|G, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1522_G|A, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1546_T|C, 1549_C|T, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A,
1579_C|T, 1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1609_CT|TC, 1618_G|A, 1621_A|T, 1642_G|T, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1701_G|A, 1705_AC|GT, 1708_G|A,
1714_G|C, 1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1781_G|A, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G,
1810_A|G, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_AT|GC, 1841_T|C, 1843_G|C, 1852_G|A, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|C, 1984_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2077_C|T,
2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G,
2200_C|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2467_C|A, 2470_C|A, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|G, 3040_C|T, 3043_T|A, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3094_C|T, 3098_T|C, 3100_G|A,
3104_G|A, 3107_T|C, 3109_A|G, 3112_T|C, 3121_G|A, 3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G,
3229_A|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_C|A, 3321_A|G, 3334_G|T, 3337_A|G,
3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G,
3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3607_A|G,
3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C,
3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3748_T|C, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G,
3832_A|C, 3844_G|A, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|G, 3898_T|C, 3901_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3955_G|A, 3959_C|T,
3961_C|G, 3973_G|A, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C,
4087_T|C, 4090_G|A, 4105_C|G, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T,
4219_A|C, 4228_GC|CT, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4270_T|C, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4324_G|A, 4330_G|A, 4333_A|T,
4336_G|A, 4341_A|G, 4351_T|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A,
4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C,
5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5047_C|T, 5059_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 7039_T|C, 7046_T|C,
7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|C, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C,
7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7666_A|G,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7696_C|T, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7732_T|C, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC,
7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7873_C|T, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T,
7900_T|C, 7915_G|A, 7918_A|G, 7920_AG|GA, 7924_A|G, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8048_G|A, 8050_G|A, 8053_A|G, 8059_C|T, 8063_C|T, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8152_.|A, 8155, 8161_G|C, 8167_C|G, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8221_G|A, 8224_A|G, 8245_C|T, 8251_A|G,
8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8317_C|T, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8407_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8764_A|G, 8773_C|T,
8782_G|A, 8788_C|T, 8792_C|T, 8815_A|G, 8830_A|G, 8833_A|G, 8836_T|C, 8839_T|A, 8848_C|T, 8851_A|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8954_A|C, 8956_GAA|ACG,
8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G,
9157_A|G, 9160_G|T, 9166_C|T, 9169_T|C, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9524_G|A, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C,
9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|C, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T,
9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9772_C|T, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T,
9850_CA|GG, 9856_G|C, 9859_A|G, 9862_A|G, 9865_G|A, 9880_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|A, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9985_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10048_A|G, 10051_G|A, 10066_G|A, 10096_A|G, 10111_C|T, 10116_A|G, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10144_A|G, 10148_A|C, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C

Case 3 (A.1): PV710596.1


Target: 835 samples Number of changes: 1413
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1410-1413Gap history (edge excluded): 34-1410
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1410 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G,
1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T,
2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_GA|CC, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G,
2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2470_C|A, 2488_G|A, 2497_C|T, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G,
2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G,
2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A,
2947_A|C, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G,
3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3109_A|T, 3112_T|C, 3121_G|A, 3127_G|A, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C,
3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C,
3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C,
3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C,
3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A,
3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G,
3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C,
3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T,
4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A,
4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C,
4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T,
4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A, 4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA,
4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A,
4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C,
4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G,
4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A,
5029_C|T, 5038_C|A, 5041_C|T, 5055_A|C, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA,
5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C,
5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A,
5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T,
5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A,
5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T,
5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C,
6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G,
6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T,
6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G,
6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A,
6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C,
6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T,
6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T,
6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T,
7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A,
7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G,
7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G,
7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C,
7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A,
7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C, 7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C,
7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G,
8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T,
8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G,
8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A,
8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T,
8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A,
8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A,
8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010,
9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9181_C|T,
9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT,
9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G,
9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T,
9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C,
9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G,
9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG,
10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A,
10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C,
10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710593.1


Target: 835 samples Number of changes: 1427
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1424-1427Gap history (edge excluded): 34-1424
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1424 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 900_A|G,
904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T,
1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT,
1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1540_C|T, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A,
1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
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9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A,
9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G,
9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C,
9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T,
10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C,
10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C,
10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710595.1


Target: 835 samples Number of changes: 1404
BC: A.1 + A.1.NmC2 + A.1 BC BR: 302-303, 1400-1401 BC BR coord: 2265 - 2266, 10363 - 10364
Direction L1: << Initial region span: 1-3,1076-1400,1401-1404Gap history (edge excluded): 3-1401 -> 3-1076
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.01e-18
Rec. model vs L1: 2.84e+14Rec. model vs L2: 1.23e-153
Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 3 0.799365 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1076 38.511947 NaN NaN NaN * * *
A.1.NmC1 0 1401 0.000000 -454.253414 3316.506827 9.479136e-195
A.1 835 1401 0.000000 -87.842653 2583.685306 1.278232e-35
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1401 2.087133 None None None * * *



Target sequence

, 112_C|A, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T,
613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A,
769_T|C, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G,
904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T,
1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1426_T|C, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1681_T|C, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T,
1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G,
1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA,
1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C,
2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA,
2197_A|G, 2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A,
2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T,
2470_C|A, 2488_G|A, 2497_C|T, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G,
2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A,
2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2899_C|G, 2908_T|C, 2920_G|A, 2962_C|T, 2980_C|T,
2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3100_G|A, 3104_G|A,
3109_A|T, 3112_T|C, 3127_G|A, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G,
3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C,
3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C,
3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC,
3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T,
3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A,
3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T,
4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A,
4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A,
4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T,
4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G,
4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T,
4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A,
5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C,
5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A,
5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG,
6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T,
6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G,
6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T,
7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T,
7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C,
7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C,
7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A,
8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A,
8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G,
8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G,
8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A,
9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A,
9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T,
9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C,
9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T,
9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T,
9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C,
9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA,
10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C,
10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G,
10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710597.1


Target: 835 samples Number of changes: 1428
BC: A.1 + A.1.NmC2 + A.1 BC BR: 387-388, 1424-1425 BC BR coord: 2895 - 2896, 10363 - 10364
Direction L1: << Initial region span: 1-14,1100-1424,1425-1428Gap history (edge excluded): 14-1425 -> 14-1100
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.53e-49
Rec. model vs L1: 1.96e+13Rec. model vs L2: 5.24e-163
Flags: Model_2BP_Best

A.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 15 0.465183 None None None * * *
|||||

A.1.NmC2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC2 0 1100 36.39528 NaN NaN NaN * * *
A.1.NmC1 0 1425 0.00000 -484.242927 3214.485855 2.503524e-208
A.1 835 1425 0.00000 -83.695622 2413.391243 2.265721e-34
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1425 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 268_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G,
346_A|G, 352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C,
467_T|C, 473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T,
613_A|C, 628_T|C, 640_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C,
766_G|A, 769_T|C, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T,
890_A|G, 904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A,
1054_A|G, 1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1144_G|A, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C,
1195_C|T, 1207_A|T, 1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A,
1306_G|A, 1321_C|T, 1327_A|G, 1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1564_G|A, 1570_A|G, 1572_C|A,
1585_A|T, 1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T,
1723_G|A, 1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G,
1813_T|C, 1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA,
1936_G|A, 1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2008_T|C, 2011_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C,
2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_GA|CC, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T,
2188_A|G, 2193_TG|CA, 2197_A|G, 2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2263_T|C, 2266_G|A, 2272_A|C, 2275_T|A,
2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C,
2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A,
2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A,
2729_C|T, 2734_G|A, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A,
2863_A|G, 2878_A|G, 2881_C|T, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T,
3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|T, 3112_T|C, 3121_G|A,
3127_G|A, 3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G,
3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C,
3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C,
3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC,
3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T,
3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A,
3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3955_G|A, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A,
4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4099_C|T,
4103_C|T, 4105_C|A, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C,
4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T,
4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A,
4495_T|C, 4498_G|A, 4504_CC|TA, 4522_TC|CT, 4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T,
4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C,
4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G,
4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A,
4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A,
5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C,
5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G,
5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C,
5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G,
5590_T|C, 5602_A|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5689_A|G, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A,
5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A,
5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C,
6067_G|A, 6073_C|T, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G,
6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T,
6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T,
6489_CT|TC, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C,
6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T,
6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T,
6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C,
7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C,
7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T,
7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C,
7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_TC|CT, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G,
7657_TT|CC, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A,
7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T,
7891_A|T, 7894_C|T, 7900_T|C, 7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G,
7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A,
8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T,
8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A,
8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA,
8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G,
8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C,
8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G,
8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C,
9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G,
9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC,
9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G,
9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T,
9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A,
9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G,
9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G,
10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|G,
10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G,
10361_A|G, 10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710599.1


Target: 835 samples Number of changes: 1402
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1399-1402Gap history (edge excluded): 34-1399
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1399 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1519_C|T, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T,
1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A,
1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T,
2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G,
2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2470_C|A,
2488_G|A, 2497_C|T, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C,
2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T,
2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2887_T|C, 2899_C|G, 2908_T|C, 2920_G|A, 2962_C|T, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3100_G|A, 3104_G|A, 3109_A|T,
3112_T|C, 3127_G|A, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A,
3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G,
3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T,
3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA,
4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T, 4120_CT|AC,
4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C,
4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T,
4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A, 4504_CC|TA, 4523_C|T,
4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C,
4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C,
4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A,
4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T,
4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A,
5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A,
5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5341_C|T,
5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A,
5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5614_C|T, 5626_G|T, 5638_CC|TT,
5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C,
5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C,
5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T,
6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_TT|AC, 6250_G|A,
6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C,
6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C,
6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T,
6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G,
6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G,
6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C,
7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G,
7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C,
7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G,
7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G,
7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C,
7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C, 7909_T|C, 7912_T|A,
7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T,
8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G,
8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T,
8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T,
8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A,
8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T,
8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A,
8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A,
8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C,
9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G,
9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C,
9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C,
9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T,
9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A,
9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T,
9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C,
10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G,
10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G,
10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710600.1


Target: 835 samples Number of changes: 1421
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1418-1421Gap history (edge excluded): 34-1418
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1418 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1732_C|T,
1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T,
2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_GA|CC, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA,
2197_A|G, 2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2266_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C,
2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C,
2464_C|T, 2467_C|A, 2470_C|A, 2488_G|A, 2497_C|T, 2500_A|G, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T,
2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2704_G|A, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2734_G|A, 2737_TG|CA,
2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2791_T|C, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T,
2894_C|A, 2896_G|A, 2899_C|G, 2908_T|C, 2920_G|A, 2932_G|A, 2947_A|C, 2950_C|A, 2962_C|T, 2974_A|G, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3013_G|A, 3019_C|T, 3025_A|G,
3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3070_A|G, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3098_T|C, 3100_G|A, 3104_G|A, 3107_T|C, 3109_A|T, 3112_T|C, 3121_G|A, 3127_G|A,
3133_A|G, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3199_C|T, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A,
3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G,
3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T,
3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA,
4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T, 4105_C|G,
4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A,
4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A,
4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T,
4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G,
4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T,
4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A,
5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C,
5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A,
5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG,
6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T,
6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G,
6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T,
7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T,
7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C,
7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_TC|CT, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G,
7669_C|T, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T,
7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T,
7900_T|C, 7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G,
8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A,
8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A,
8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G,
8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G,
8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A,
8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT, 8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A,
8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT, 8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T,
8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G, 8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C,
9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A,
9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T, 9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T,
9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT, 9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G,
9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A, 9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T,
9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A, 9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G,
9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T, 9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T,
9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C, 10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG,
10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T, 10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C,
10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G, 10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C,
10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710602.1


Target: 835 samples Number of changes: 1402
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1399-1402Gap history (edge excluded): 34-1399
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1399 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G,
1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C,
2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2209_C|T, 2215_A|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T,
2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2470_C|A, 2488_G|A, 2497_C|T,
2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G,
2644_G|A, 2687_T|C, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2770_A|G, 2773_T|A, 2776_G|T, 2782_T|C,
2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2899_C|G, 2908_T|C, 2920_G|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T,
2998_T|C, 3002_T|C, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3100_G|A, 3104_G|A, 3109_A|T, 3112_T|C, 3127_G|A,
3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G,
3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A,
3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G,
3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T,
3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC,
3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C,
3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA,
4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C,
4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T,
4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A, 4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C,
4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A,
4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C,
4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C,
4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A,
5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T,
5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A,
5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C,
5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T,
6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A,
6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G,
7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A,
7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C, 7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA,
7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G,
8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G,
8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT,
8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9046_G|A, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T,
9166_C|T, 9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710603.1


Target: 835 samples Number of changes: 1400
BC: A.1.NmC1 + A.1 BC BR: 52-53 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1397-1400Gap history (edge excluded): 34-1397
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.88e+12
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1397 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T, 613_A|C,
628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A, 769_T|C,
775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G, 904_T|G,
910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G, 1072_T|G,
1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T, 1210_G|A,
1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T, 1327_A|G,
1330_C|T, 1333_T|C, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T, 1482_TC|CT, 1491_T|C,
1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T, 1591_C|T, 1593_G|A,
1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A, 1729_C|A, 1738_A|G,
1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C, 1816_TT|CG,
1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A, 1942_A|G, 1946_T|C,
1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T, 2080_A|T, 2083_T|C,
2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G, 2209_C|T, 2215_A|T,
2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A, 2308_A|G, 2314_C|T,
2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2470_C|A, 2488_G|A, 2497_C|T,
2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2605_A|G, 2611_G|A, 2623_A|G, 2626_T|C, 2632_T|C, 2641_T|G,
2644_G|A, 2687_T|C, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A, 2776_G|T, 2782_T|C, 2785_G|A,
2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2899_C|G, 2908_T|C, 2920_G|A, 2962_C|T, 2980_C|T, 2983_A|G, 2986_C|T, 2989_C|T, 2998_T|C,
3002_T|C, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3100_G|A, 3104_G|A, 3109_A|T, 3112_T|C, 3127_G|A, 3142_T|C,
3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G, 3280_G|A, 3283_A|G, 3298_G|A,
3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA, 3373_T|C, 3397_C|A, 3409_G|A,
3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A, 3502_T|G, 3505_A|G, 3514_A|G,
3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A, 3628_A|C, 3632_C|T, 3634_G|A,
3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G, 3718_C|T, 3733_GT|CC, 3739_T|C,
3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T, 3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A,
3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA, 4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T,
4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4103_C|T, 4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C,
4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G, 4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A,
4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A, 4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T,
4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A, 4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C,
4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T, 4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A,
4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G, 4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C,
4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A, 4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C,
4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T, 4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C,
4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G, 5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A,
5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A, 5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T,
5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C, 5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C,
5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A, 5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A,
5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T, 5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C,
5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A, 5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T,
5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C, 5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T,
6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A, 6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A,
6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C, 6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C,
6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G, 6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G,
6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG, 6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G,
6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T, 6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G,
6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G, 6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G,
6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G, 6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A,
6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T, 7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T,
7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T, 7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T,
7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T, 7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C,
7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C, 7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G,
7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T, 7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A,
7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A, 7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A,
7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C, 7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA,
7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G, 8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G,
8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C, 8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A,
8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T, 8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G,
8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A, 8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8422_G|A,
8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G, 8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G,
8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A, 8593_G|A, 8600_G|A, 8602_A|T, 8605_T|C, 8608_T|G, 8611_T|G, 8614_T|C, 8617_A|G, 8620_TC|CT,
8629_T|C, 8632_A|C, 8650_G|A, 8656_A|G, 8671_T|A, 8680_C|T, 8692_G|A, 8704_T|C, 8707_A|G, 8743_G|A, 8746_A|G, 8749_T|C, 8755_G|A, 8758_C|T, 8764_A|G, 8782_G|A, 8788_C|T, 8792_C|T, 8815_AC|GT,
8830_A|G, 8833_A|G, 8839_T|A, 8848_C|T, 8851_A|C, 8866_T|C, 8874_A|T, 8884_A|G, 8911_G|A, 8923_C|T, 8926_A|G, 8939_C|T, 8941_G|A, 8954_A|C, 8956_GAA|ACG, 8965_C|T, 8968_A|G, 8971_A|G,
8980_T|C, 8983_G|A, 9009_9010, 9017_.|AA, 9037_G|A, 9040_A|G, 9043_A|G, 9061_A|C, 9067_T|C, 9082_G|C, 9085_G|A, 9100_G|A, 9127_T|C, 9133_T|A, 9142_A|G, 9151_A|G, 9157_A|G, 9160_G|T, 9166_C|T,
9172_CT|TC, 9181_C|T, 9187_A|C, 9190_T|C, 9199_A|G, 9212_A|C, 9214_G|A, 9217_T|G, 9232_C|T, 9244_C|A, 9259_G|A, 9265_C|A, 9274_A|G, 9277_C|T, 9280_T|G, 9295_G|A, 9319_T|C, 9322_C|T,
9324_AA|GG, 9328_AC|GT, 9334_A|G, 9336_A|T, 9340_A|T, 9343_G|A, 9361_G|A, 9379_GT|CC, 9385_A|G, 9391_C|T, 9397_A|T, 9406_C|T, 9424_T|C, 9427_A|G, 9430_A|G, 9454_A|G, 9463_T|C, 9466_TC|CT,
9485_T|C, 9490_A|G, 9493_C|T, 9497_T|C, 9502_C|T, 9505_A|G, 9514_A|G, 9532_T|C, 9538_A|G, 9544_T|C, 9547_A|G, 9550_T|C, 9556_T|C, 9559_AT|CA, 9562_A|G, 9566_C|T, 9573_G|A, 9577_G|T, 9580_G|A,
9590_A|G, 9598_C|T, 9601_A|C, 9604_T|C, 9610_A|G, 9613_G|T, 9625_G|A, 9637_C|T, 9646_G|T, 9652_G|A, 9658_C|T, 9670_C|T, 9679_C|T, 9691_C|T, 9694_C|T, 9703_C|A, 9709_TA|GC, 9715_G|A, 9745_G|A,
9749_A|G, 9754_T|C, 9762_A|G, 9775_T|C, 9778_C|T, 9787_C|T, 9796_A|G, 9799_G|A, 9817_G|A, 9823_G|A, 9835_A|G, 9838_A|T, 9841_G|A, 9844_C|T, 9850_CA|GG, 9856_G|C, 9862_A|G, 9865_G|A, 9880_C|T,
9883_C|T, 9898_A|G, 9904_T|A, 9910_C|T, 9916_A|G, 9919_C|T, 9922_T|C, 9946_T|C, 9955_A|G, 9970_A|G, 9973_G|T, 9977_T|C, 9988_C|T, 9991_A|T, 10003_C|A, 10006_A|T, 10018_A|G, 10027_A|C,
10030_A|G, 10036_GA|TG, 10066_G|A, 10096_A|G, 10111_C|T, 10126_C|T, 10129_G|A, 10132_A|G, 10134_T|C, 10141_AA|GG, 10153_TG|CA, 10162_T|C, 10165_A|G, 10177_A|G, 10186_G|T, 10189_C|T,
10204_A|G, 10213_T|C, 10216_G|A, 10222_C|T, 10228_C|A, 10231_C|T, 10240_T|C, 10243_A|G, 10246_C|A, 10249_C|A, 10252_T|C, 10255_T|C, 10261_A|G, 10264_G|A, 10273_AC|GA, 10276_G|A, 10281_A|G,
10297_A|G, 10309_C|T, 10315_T|C, 10330_C|T, 10336_A|G, 10338_TG|CC, 10348_T|C, 10351_C|T, 10355_A|G, 10361_A|G, 10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C

Case 3 (A.1): PV710604.1


Target: 835 samples Number of changes: 1406
BC: A.1.NmC1 + A.1 BC BR: 53-54 BC BR coord: 552 - 553
Direction L1: >> Initial region span: 1-34,1403-1406Gap history (edge excluded): 34-1403
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.09e+18
Flags: Model_2BP_Bad_L1_opp

A.1.NmC1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1.NmC1 0 34 2.30746 None None None * * *
|||||

A.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.1 835 1403 2.087133 None None None * * *



Target sequence

, 116_A|C, 119_A|C, 166_A|T, 178_T|C, 192_A|G, 225_AC|GT, 247_T|C, 260_A|G, 262_C|T, 281_A|G, 295_A|G, 301_C|T, 304_A|C, 307_C|T, 310_C|T, 313_A|G, 318_GGT|AAC, 322_G|A, 327_A|G, 346_A|G,
352_G|A, 354_C|T, 358_T|C, 361_A|G, 367_A|G, 370_C|T, 376_A|G, 385_C|G, 389_T|C, 400_A|T, 409_A|G, 421_T|A, 427_T|A, 434_C|T, 436_G|A, 440_G|A, 442_G|A, 448_CC|TT, 451_A|G, 455_T|C, 467_T|C,
473_ACG|GTT, 488_T|C, 493_G|A, 496_G|C, 498_A|G, 511_G|A, 514_C|T, 517_A|G, 523_G|T, 538_C|T, 547_A|C, 551_T|C, 556_G|T, 577_A|C, 584_T|C, 589_A|G, 595_G|A, 598_C|T, 604_C|T, 610_C|T,
613_A|C, 628_T|C, 649_G|A, 655_A|T, 664_T|A, 667_T|C, 670_C|T, 682_G|A, 691_C|T, 694_T|C, 703_A|T, 709_T|C, 718_C|T, 724_A|G, 727_C|T, 733_T|A, 736_G|A, 742_A|C, 760_G|A, 763_T|C, 766_G|A,
769_T|C, 775_C|T, 781_T|C, 784_G|A, 802_A|G, 823_T|C, 826_A|G, 829_G|A, 832_A|G, 835_C|G, 838_A|G, 841_G|A, 847_G|A, 854_T|C, 856_C|G, 871_T|C, 877_A|G, 879_TG|CA, 883_G|A, 887_C|T, 890_A|G,
904_T|G, 910_A|G, 931_C|T, 934_G|C, 937_T|C, 943_A|G, 946_G|A, 961_T|C, 964_G|A, 970_C|T, 973_A|G, 985_T|A, 991_T|A, 994_T|C, 1024_A|G, 1030_T|C, 1042_T|C, 1046_C|T, 1051_G|A, 1054_A|G,
1072_T|G, 1081_T|C, 1094_T|C, 1096_G|A, 1102_C|A, 1111_G|A, 1117_A|T, 1127_A|G, 1140_TG|CA, 1147_A|G, 1153_T|C, 1158_A|G, 1165_TC|CT, 1168_C|G, 1171_TC|CA, 1174_T|C, 1195_C|T, 1207_A|T,
1210_G|A, 1217_C|T, 1219_A|G, 1221_CT|AA, 1228_G|A, 1231_C|T, 1237_G|A, 1246_G|T, 1255_C|A, 1261_T|C, 1264_T|C, 1273_C|T, 1279_C|A, 1285_C|T, 1292_C|T, 1294_A|G, 1300_G|A, 1306_G|A, 1321_C|T,
1327_A|G, 1330_C|T, 1333_T|C, 1339_C|T, 1352_T|C, 1354_G|A, 1390_C|T, 1393_A|G, 1399_AT|GC, 1402_G|A, 1408_A|C, 1411_G|A, 1423_A|G, 1432_T|C, 1435_C|T, 1441_T|C, 1444_G|A, 1474_C|T,
1482_TC|CT, 1491_T|C, 1495_G|A, 1498_T|C, 1501_A|G, 1503_AA|GG, 1507_T|C, 1516_A|G, 1525_G|A, 1528_A|G, 1531_T|C, 1534_G|A, 1543_TG|CA, 1558_C|T, 1561_T|A, 1570_A|G, 1572_C|A, 1585_A|T,
1591_C|T, 1593_G|A, 1606_G|A, 1610_T|C, 1618_G|A, 1621_A|T, 1642_G|C, 1666_T|C, 1669_C|G, 1678_A|G, 1684_G|A, 1690_C|T, 1693_C|A, 1696_T|C, 1701_G|A, 1705_AC|GT, 1708_G|A, 1714_G|T, 1723_G|A,
1729_C|A, 1738_A|G, 1741_A|T, 1747_T|C, 1753_C|T, 1760_A|C, 1762_G|A, 1765_T|C, 1771_G|A, 1780_TG|CA, 1785_A|G, 1789_C|G, 1792_T|G, 1795_C|T, 1798_A|G, 1801_A|G, 1807_T|G, 1810_A|G, 1813_T|C,
1816_TT|CG, 1819_T|G, 1822_C|T, 1825_A|G, 1831_A|G, 1841_T|C, 1843_G|C, 1849_C|T, 1855_G|A, 1867_A|G, 1870_A|G, 1873_C|T, 1876_T|C, 1887_T|C, 1894_C|T, 1915_C|A, 1926_TT|CA, 1936_G|A,
1942_A|G, 1946_T|C, 1957_C|A, 1975_G|A, 1978_A|G, 1981_A|T, 1984_T|C, 1993_T|C, 2003_A|G, 2017_T|C, 2023_T|C, 2029_T|C, 2032_C|T, 2035_C|A, 2038_C|A, 2044_A|C, 2063_C|T, 2068_T|C, 2077_C|T,
2080_A|T, 2083_T|C, 2089_A|G, 2092_C|T, 2095_C|T, 2101_T|C, 2104_C|A, 2112_G|C, 2116_A|G, 2125_T|C, 2128_C|G, 2146_A|G, 2149_G|A, 2152_A|C, 2164_A|G, 2173_C|T, 2188_A|G, 2193_TG|CA, 2197_A|G,
2209_C|T, 2215_A|T, 2218_CA|TG, 2221_C|T, 2230_T|C, 2233_CA|TG, 2236_C|T, 2239_C|T, 2248_G|A, 2257_T|A, 2260_G|A, 2272_A|C, 2275_T|A, 2278_T|C, 2281_G|T, 2299_T|C, 2302_G|A, 2305_G|A,
2308_A|G, 2314_C|T, 2322_A|G, 2349_CG|TA, 2353_A|C, 2356_T|C, 2371_C|T, 2380_A|G, 2383_C|T, 2408_T|C, 2410_G|A, 2413_A|T, 2419_G|C, 2431_TT|CC, 2437_T|C, 2455_T|C, 2464_C|T, 2470_C|A,
2488_G|A, 2497_C|T, 2506_T|C, 2513_A|G, 2515_A|C, 2524_C|T, 2527_T|A, 2548_C|T, 2563_A|G, 2566_T|C, 2569_T|A, 2572_G|A, 2575_G|A, 2581_A|T, 2596_C|T, 2599_T|C, 2605_A|G, 2611_G|A, 2623_A|G,
2626_T|C, 2632_T|C, 2641_T|G, 2644_G|A, 2687_T|C, 2698_C|T, 2710_T|C, 2713_T|A, 2716_T|G, 2719_C|G, 2722_G|C, 2725_G|A, 2729_C|T, 2737_TG|CA, 2743_C|T, 2752_A|G, 2755_T|A, 2761_A|G, 2773_T|A,
2776_G|T, 2782_T|C, 2785_G|A, 2788_G|A, 2794_T|C, 2809_T|C, 2812_G|A, 2827_C|T, 2833_G|A, 2836_G|A, 2863_A|G, 2878_A|G, 2881_C|T, 2899_C|G, 2908_T|C, 2920_G|A, 2962_C|T, 2980_C|T, 2983_A|G,
2986_C|T, 2989_C|T, 2998_T|C, 3002_T|C, 3019_C|T, 3025_A|G, 3031_T|C, 3034_C|A, 3040_C|G, 3043_T|C, 3052_T|C, 3064_T|C, 3073_A|G, 3079_G|A, 3091_C|T, 3094_C|T, 3100_G|A, 3104_G|A, 3109_A|T,
3112_T|C, 3127_G|A, 3142_T|C, 3172_A|C, 3178_C|T, 3187_A|G, 3193_C|T, 3196_A|G, 3211_T|C, 3217_T|C, 3220_T|C, 3223_C|T, 3226_T|G, 3232_C|T, 3238_T|C, 3244_G|A, 3253_T|C, 3265_A|G, 3274_A|G,
3280_G|A, 3283_A|G, 3298_G|A, 3301_T|C, 3304_C|T, 3308_A|G, 3310_CA|TG, 3316_T|C, 3319_CAA|AGG, 3331_A|G, 3334_G|T, 3337_A|G, 3340_A|G, 3343_A|G, 3352_C|G, 3358_G|T, 3361_T|C, 3370_AG|GA,
3373_T|C, 3397_C|A, 3409_G|A, 3412_T|A, 3424_T|C, 3427_T|G, 3436_G|T, 3439_T|C, 3445_T|C, 3448_C|T, 3454_A|G, 3460_G|A, 3465_G|A, 3469_A|G, 3472_G|A, 3478_A|C, 3484_T|C, 3490_G|C, 3496_C|A,
3502_T|G, 3505_A|G, 3514_A|G, 3517_A|C, 3523_TG|AA, 3529_T|C, 3535_T|G, 3556_A|C, 3566_G|A, 3568_CC|AT, 3571_A|G, 3577_A|G, 3589_A|C, 3598_GT|AC, 3610_AG|CA, 3613_A|G, 3619_CT|TC, 3622_G|A,
3628_A|C, 3632_C|T, 3634_G|A, 3637_C|T, 3640_G|A, 3643_A|G, 3646_A|G, 3650_C|A, 3653_C|T, 3655_T|G, 3658_T|C, 3667_A|G, 3679_T|G, 3682_G|T, 3686_T|C, 3691_T|C, 3694_C|T, 3706_C|T, 3715_A|G,
3718_C|T, 3733_GT|CC, 3739_T|C, 3745_C|T, 3781_GC|AT, 3784_C|G, 3790_C|G, 3793_A|G, 3802_T|C, 3805_G|A, 3814_T|C, 3826_A|G, 3829_A|G, 3832_A|C, 3850_C|T, 3860_G|A, 3868_C|A, 3871_C|T,
3883_T|C, 3886_A|G, 3889_T|C, 3895_T|A, 3898_T|C, 3901_C|T, 3904_C|T, 3928_T|C, 3931_T|C, 3934_G|A, 3947_AC|GT, 3953_T|C, 3959_C|T, 3961_C|G, 3968_C|T, 3982_C|G, 3985_T|A, 4006_CG|AA,
4013_T|C, 4018_T|C, 4021_TG|CA, 4024_C|T, 4030_T|C, 4036_A|C, 4039_G|C, 4042_C|T, 4045_T|C, 4048_C|T, 4054_T|C, 4056_TC|CA, 4066_C|T, 4081_T|C, 4087_T|C, 4089_T|A, 4099_C|T, 4103_C|T,
4120_CT|AC, 4126_A|G, 4129_A|G, 4132_T|C, 4135_T|C, 4142_C|T, 4150_A|C, 4153_TC|CA, 4165_C|A, 4171_T|C, 4183_T|C, 4198_G|A, 4201_A|G, 4204_C|T, 4210_A|T, 4219_A|C, 4228_G|C, 4237_A|G,
4240_G|A, 4246_T|C, 4258_G|A, 4261_C|T, 4264_C|T, 4267_T|A, 4273_GA|AG, 4276_T|C, 4289_C|A, 4306_T|C, 4309_C|T, 4330_G|A, 4333_A|T, 4336_G|A, 4341_A|G, 4351_T|G, 4360_A|T, 4369_G|A, 4372_G|A,
4375_G|T, 4384_C|T, 4387_G|A, 4393_C|T, 4399_C|T, 4409_GCA|ATT, 4420_A|G, 4429_G|A, 4432_C|T, 4435_G|A, 4438_G|A, 4441_T|C, 4453_A|G, 4465_C|T, 4480_C|T, 4483_G|A, 4495_T|C, 4498_G|A,
4504_CC|TA, 4523_C|T, 4526_C|T, 4531_C|T, 4540_G|C, 4544_C|T, 4549_T|C, 4552_T|C, 4557_GG|AA, 4564_T|C, 4567_G|A, 4583_T|C, 4585_G|T, 4600_T|A, 4606_G|A, 4612_C|T, 4618_A|G, 4625_C|T,
4630_G|A, 4639_G|A, 4642_T|C, 4645_T|C, 4654_C|T, 4663_C|A, 4666_CT|TC, 4669_G|A, 4678_C|T, 4681_G|A, 4684_A|G, 4699_A|G, 4711_G|C, 4714_C|T, 4720_A|G, 4729_T|C, 4735_AA|GC, 4741_A|G,
4744_T|C, 4747_C|T, 4750_T|C, 4753_C|T, 4756_G|A, 4759_T|C, 4762_C|T, 4765_G|A, 4769_T|C, 4772_A|G, 4780_T|C, 4786_T|C, 4792_A|C, 4807_C|T, 4810_C|T, 4816_T|C, 4834_A|G, 4837_C|T, 4852_G|A,
4855_A|G, 4861_C|T, 4870_C|A, 4873_G|A, 4878_TT|CC, 4882_A|C, 4888_G|A, 4897_C|G, 4900_C|T, 4906_G|A, 4912_A|G, 4915_G|A, 4919_T|C, 4921_G|A, 4927_A|G, 4930_G|T, 4939_G|A, 4954_T|G, 4957_C|T,
4960_T|C, 4969_T|C, 4984_A|T, 4987_A|T, 4993_T|C, 4996_T|C, 4999_T|C, 5008_C|T, 5011_A|T, 5017_G|A, 5020_T|A, 5029_C|T, 5038_C|A, 5041_C|T, 5062_C|T, 5068_C|T, 5080_G|A, 5092_G|A, 5095_A|G,
5098_A|G, 5101_A|G, 5104_G|A, 5113_C|A, 5116_A|G, 5119_G|A, 5132_C|T, 5134_A|G, 5143_A|G, 5152_TG|CA, 5155_C|T, 5164_T|C, 5182_G|A, 5194_C|T, 5197_C|T, 5200_A|T, 5207_T|C, 5212_C|T, 5215_G|A,
5224_G|A, 5230_C|G, 5239_T|A, 5246_T|C, 5251_C|T, 5254_C|T, 5257_C|T, 5260_G|A, 5266_T|C, 5269_T|C, 5284_G|A, 5287_T|C, 5296_CC|TT, 5299_G|A, 5302_C|T, 5305_G|C, 5308_A|G, 5311_C|T, 5326_T|C,
5335_C|T, 5338_C|T, 5341_C|T, 5344_G|A, 5346_G|A, 5359_T|C, 5362_C|T, 5368_C|T, 5380_A|G, 5383_T|A, 5389_G|A, 5404_T|C, 5407_G|A, 5410_T|G, 5413_T|C, 5416_C|T, 5431_T|C, 5437_T|C, 5443_C|A,
5452_G|A, 5458_A|G, 5470_C|A, 5473_T|C, 5485_A|G, 5488_G|A, 5491_C|T, 5497_T|C, 5500_G|A, 5530_A|T, 5536_A|C, 5539_G|T, 5542_T|G, 5545_G|A, 5548_T|C, 5575_T|G, 5584_A|G, 5590_T|C, 5602_A|T,
5614_C|T, 5626_G|T, 5638_CC|TT, 5641_A|G, 5644_T|G, 5662_A|C, 5668_C|T, 5683_A|G, 5686_T|A, 5701_T|A, 5713_T|C, 5716_G|A, 5737_C|G, 5740_G|A, 5760_G|A, 5773_G|A, 5776_A|T, 5779_G|A, 5785_G|A,
5794_C|T, 5797_T|C, 5800_A|C, 5818_T|C, 5821_A|G, 5833_C|T, 5836_T|C, 5846_C|A, 5852_C|T, 5860_C|T, 5872_T|C, 5875_G|A, 5899_G|A, 5923_T|C, 5926_T|G, 5932_C|A, 5935_A|T, 5941_T|C, 5947_T|C,
5968_G|A, 5971_A|G, 5974_T|C, 5980_C|T, 5986_T|C, 5992_C|T, 6004_T|C, 6013_T|C, 6023_A|G, 6025_T|C, 6031_C|G, 6034_C|T, 6037_C|T, 6047_T|C, 6049_G|T, 6065_T|C, 6067_G|A, 6073_C|T, 6085_G|A,
6091_A|G, 6097_C|T, 6100_C|T, 6106_C|T, 6113_G|A, 6115_T|A, 6124_T|A, 6127_A|G, 6139_C|T, 6154_A|G, 6157_G|A, 6160_G|A, 6174_A|G, 6182_A|C, 6187_A|G, 6190_A|G, 6199_T|C, 6211_C|T, 6220_T|C,
6223_G|A, 6244_TT|AC, 6250_G|A, 6259_T|C, 6262_T|A, 6271_T|C, 6277_A|G, 6283_T|A, 6286_G|A, 6310_C|T, 6316_A|G, 6322_G|A, 6331_G|A, 6334_T|C, 6346_A|C, 6361_C|T, 6365_A|C, 6373_T|C, 6388_A|G,
6406_GT|TG, 6409_T|C, 6412_A|C, 6415_T|C, 6418_T|A, 6430_A|G, 6433_T|C, 6439_G|A, 6442_A|G, 6451_AG|GA, 6457_A|G, 6460_T|C, 6478_T|A, 6481_T|C, 6485_C|T, 6489_CT|TC, 6493_A|G, 6508_AA|GG,
6517_C|T, 6520_C|T, 6523_T|C, 6527_T|C, 6530_C|T, 6532_C|G, 6547_C|T, 6550_T|C, 6553_G|A, 6569_C|T, 6571_A|G, 6597_T|C, 6611_A|G, 6613_A|T, 6619_T|C, 6622_A|G, 6625_A|G, 6631_A|G, 6634_G|T,
6643_C|T, 6664_A|G, 6667_C|T, 6673_T|C, 6688_G|A, 6697_A|G, 6703_C|T, 6706_C|T, 6715_T|C, 6724_C|T, 6745_T|C, 6754_C|T, 6757_TG|CA, 6766_C|A, 6779_C|T, 6794_A|G, 6796_C|T, 6799_C|G, 6805_A|G,
6811_A|G, 6814_A|G, 6817_GT|AA, 6823_C|T, 6826_A|G, 6832_C|T, 6835_A|G, 6841_A|T, 6844_C|T, 6847_C|T, 6850_T|C, 6853_T|A, 6869_G|A, 6874_A|T, 6876_C|T, 6889_C|T, 6892_G|A, 6907_G|A, 6910_A|G,
6913_C|T, 6916_A|G, 6919_G|A, 6931_G|A, 6934_G|A, 6940_C|T, 6943_A|G, 6948_C|T, 6958_TT|CG, 6970_T|C, 6976_G|A, 6980_C|T, 6986_C|T, 6991_G|A, 7000_T|C, 7003_C|T, 7009_A|T, 7012_G|C, 7015_C|T,
7027_T|C, 7039_T|C, 7046_T|C, 7063_A|G, 7066_C|T, 7069_A|G, 7078_C|T, 7085_C|T, 7096_A|T, 7099_C|A, 7114_CC|TT, 7117_T|G, 7120_T|A, 7135_G|T, 7138_A|C, 7141_A|G, 7144_C|T, 7156_T|C, 7171_G|T,
7174_G|A, 7201_A|G, 7210_T|C, 7216_C|T, 7225_A|T, 7228_G|A, 7240_C|T, 7247_T|A, 7255_TT|CC, 7258_A|G, 7261_T|C, 7267_C|A, 7288_T|G, 7297_A|G, 7306_C|T, 7312_C|T, 7318_CG|TA, 7324_C|T,
7327_T|G, 7351_T|C, 7366_T|C, 7369_T|G, 7384_T|C, 7396_AC|GT, 7402_TC|AT, 7405_A|G, 7411_C|T, 7414_T|G, 7420_T|C, 7423_C|T, 7427_C|T, 7429_A|G, 7432_T|C, 7447_C|T, 7453_G|A, 7463_T|C,
7480_C|G, 7483_A|G, 7492_T|A, 7496_T|C, 7498_A|G, 7501_G|A, 7510_A|C, 7519_C|T, 7552_C|G, 7579_T|C, 7597_A|T, 7612_A|C, 7624_A|G, 7642_C|A, 7651_A|G, 7654_A|G, 7657_TT|CC, 7666_A|G, 7669_C|T,
7675_G|A, 7681_A|G, 7687_T|C, 7691_T|C, 7699_G|A, 7701_GA|AG, 7712_T|C, 7721_A|C, 7726_C|A, 7744_T|C, 7750_T|C, 7753_G|A, 7756_A|T, 7760_A|C, 7762_G|A, 7765_TT|CC, 7771_C|T, 7780_G|A,
7792_G|A, 7798_G|C, 7804_C|G, 7807_G|A, 7819_G|A, 7822_A|G, 7825_G|A, 7829_T|C, 7837_G|A, 7853_C|T, 7861_T|A, 7864_G|A, 7869_T|C, 7879_G|A, 7885_C|G, 7888_C|T, 7891_A|T, 7894_C|T, 7900_T|C,
7909_T|C, 7912_T|A, 7915_G|A, 7918_A|G, 7920_AG|GA, 7936_C|T, 7939_A|G, 7945_T|C, 7948_T|C, 7956_GA|AG, 7960_C|A, 7966_T|C, 7969_G|A, 7972_A|G, 7987_A|G, 7990_T|C, 7996_A|G, 8023_A|G,
8030_A|G, 8035_C|T, 8041_A|T, 8044_A|G, 8048_G|A, 8053_A|G, 8065_TT|GC, 8071_T|C, 8086_A|G, 8089_AT|CC, 8092_G|A, 8098_G|A, 8101_C|G, 8104_A|C, 8107_G|A, 8116_G|A, 8120_G|A, 8134_T|C,
8140_A|T, 8143_A|G, 8150_C|T, 8154_CT|GC, 8161_G|C, 8167_C|A, 8169_A|G, 8188_A|G, 8203_A|T, 8209_T|G, 8212_C|T, 8215_G|A, 8218_AC|GT, 8224_A|G, 8245_C|T, 8251_A|G, 8254_G|A, 8263_C|T,
8266_T|C, 8272_C|T, 8275_G|A, 8281_C|A, 8284_T|C, 8287_T|C, 8290_A|G, 8296_C|T, 8299_C|T, 8305_T|G, 8320_TG|CA, 8326_A|G, 8329_T|C, 8338_C|T, 8354_C|T, 8356_G|A, 8374_T|C, 8377_A|G, 8380_T|A,
8383_A|C, 8392_C|T, 8395_G|T, 8398_G|A, 8401_T|C, 8404_C|T, 8413_C|T, 8422_G|A, 8434_T|G, 8437_G|A, 8446_G|A, 8452_C|A, 8455_G|T, 8458_C|T, 8460_AA|GG, 8463_AG|CA, 8470_A|T, 8476_A|G,
8485_G|A, 8488_G|A, 8500_G|A, 8505_TGA|CCG, 8510_T|A, 8518_TT|CC, 8524_C|T, 8526_A|G, 8536_C|T, 8539_C|T, 8545_C|T, 8551_C|T, 8554_C|T, 8560_C|T, 8566_T|C, 8574_A|G, 8584_A|G, 8590_G|A,
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10364_T|C, 10367_C|G, 10369_GG|AC, 10374_A|C